Ok, this is long, so I'll probably be splitting it into a couple posts...
This might sound a bit odd, but I'm fairly certain that the root of a lot of the balance problems in 3.5 is the Monster Manual. Specifically, with the way CR was handled in relation to total HD.
Throughout the MM, creatures were given additional HD (sometimes twice their CR or more) just to get their BAB and total HP up to snuff, because they happened to be a creature type that don't get a good BAB/HD. (Giants, Dire Animals, Undead, etc.)
Since a lot of other important attributes are also tied to total HD, saves, skills, and feats for instance, these high HD creatures might have appropriate statistics in terms of physical combat, but they prevent anyone attempting to balance other areas of the game, such as spellcasting, from simply balancing them against the expected stats of normal run of the mill NPCs and players.
Without fixing this problem, it's never going to be possible to fix the rest of the class issues without either leaving everyone feeling useless against higher level mobs, or leaving them massively overpowered vs. high level humanoid NPCs.
It might be a good idea to change the BAB/HD/Saves from being tied to the creature type to being tied to a [role] or [subtype] as well. Otherwise a lot of great creature ideas are just flat out impossible to build in d20 without breaking something. For example, it might be possible to make stats for a Redcap in d20, but with d6 base hd and a wizard base attack, it would need to either have massively overinflated hd (breaking it's saves against casters) or have massively overinflated stats/abilities (breaking polymorph and making it hard to balance as a playable race).
So here's what I'm thinking of houseruling in my games...
Tie HD to CR. Period.
Creatures/types that need additional HP or fewer HP, would either have a lower or higher con, or have keyworded bonuses/penalties to hp. For example, Tough (+3 hp, +1 hp per die), Resilient (+5 hp, +2 hp per die), Weak (-3 hp, -1 hp per die), Frail (-5 hp, -2 hp per die)
Traits (special attacks, special qualities, alignment restrictions) should be determined by type/subtype.
Features (attack bonus, hit die, saves, and skill points) should be determined by role.
[word of warning, the formatting on this is going to be a bit plain until I get a chance to put it all in a PDF, sorry.]
Roles
Roles determine a creatures HD, BAB, base saving throws, and skill points per HD. The also include a list of suggested skills for use in creating new creatures of that role.
Adept
Fragile foes that rely on special abilities to survive.
HD: d6
BAB: Base attack bonus equal to 1/2 total Hit Dice (as Wizard).
Saves: Good Willpower
Skills: 2 skill points per HD
Suggested skills: Knowledge, Spellcraft, Use Magic Device
Agile
Fast moving foes that are particularly skilled at avoiding direct combat.
HD: d6
BAB: Base attack bonus equal to 1/2 total Hit Dice (as Wizard).
Saves: Good Reflex and Willpower
Skills: 4 skill points per HD
Suggested Skills: Acrobatics, Climb, Disguise, Escape Artist, Fly, Perception, Ride, Sleight of Hand, Stealth, Use Magic Device
Brawler
Basic foes capable of withstanding the rigors of combat.
HD: d10
BAB: Base attack bonus equal to total Hit Dice (as fighter).
Saves: Good Fortitude
Skills: 2 skill points per HD
Suggested skills: Intimidate
Elite
Unique and powerful foes, likely to be a challenge for even a prepared group of adventurers.
HD: d10
BAB: Base attack bonus equal to total Hit Dice (as fighter).
Saves: All Good
Skills: 8 skill points per HD
Suggested skills: All
Scout
Skilled foes able to avoid detection and perform reasonably in combat.
HD: d8
BAB: Base attack bonus equal to 3/4 total Hit Dice (as cleric).
Saves: Good Reflex
Skills: 6 skill points per HD
Suggested skills: Acrobatics, Bluff, Climb, Disable Device, Escape Artist, Linguistics, Perception, Sleight of Hand, Stealth, Survival, Swim, Use Magic Device
Skirmisher
Fast moving foes that prefer to attack from range or while moving.
HD: d10
BAB: Base attack bonus equal to total Hit Dice (as fighter).
Saves: Good Reflex
Skills: 4 skill points per HD
Suggested skills: Acrobatics, Climb, Fly, Handle Animal, Perception, Ride
Strategist
Stealthy foes capable of attacking from ambush, while still holding their own in open combat.
HD: d10
BAB: Base attack bonus equal to total Hit Dice (as fighter).
Saves: Good Fortitude and Reflex
Skills: 4 skill points per HD
Suggested skills: Acrobatics, Climb, Escape Artist, Perception, Stealth, Survival
Socialite
Talkative foes that are capable of outthinking their enemies.
HD: d8
BAB: Base attack bonus equal to 3/4 total Hit Dice (as cleric).
Saves: Good Willpower
Skills: 4 skill points per HD
Suggested skills: Appraise, Bluff, Diplomacy, Disguise, Escape Artist, Intimidate, Linguistics, Perform, Sense Motive
Specialist
Highly skilled foes that are out of their element in a direct confrontation.
HD: d6
BAB: Base attack bonus equal to 1/2 total Hit Dice (as Wizard).
Saves: Good Fortitude
Skills: 4 skill points per HD
Suggested Skills: Appraise, Bluff, Craft, Disable Device, Handle Animal, Knowledge, Linguistics, Profession, Spellcraft, Use Magic Device
Support
Generalist foes that fill in the gaps and provide useful abilities.
HD: d8
BAB: Base attack bonus equal to 3/4 total Hit Dice (as cleric).
Saves: Good Fortitude and Willpower
Skills: 4 skill points per HD
Suggested skills: Climb, Craft, Heal, Knowledge, Perception, Profession, Sense Motive, Stealth, Survival, Swim
Types & Subtypes
Types and subtypes, along with a creatures role, determine many of that creatures basic attributes and abilities. Types are listed in bold and subtypes are italicized. Subtypes that are only applicable to a specific type (such as Goblinoid or Devil) are listed with that Type, general subtypes that can be applied more broadly are listed seperately, at the end.
Aberration
An aberration has a bizarre anatomy, strange abilities, an alien mindset, or any combination of the three.
Traits:
Darkvision out to 60 feet.
Animal
An animal is a living, nonhuman creature, usually a vertebrate with no magical abilities and no innate capacity for language or culture.
Traits:
Intelligence score of 1 or 2 (no creature with an Intelligence score of 3 or higher can be an animal).
Low-light vision.
Alignment: Always neutral.
Treasure: None.
(Magical Beast)
Magical beasts are similar to natural animals but can have Intelligence scores higher than 2. Magical beasts usually have supernatural or extraordinary abilities, but sometimes are merely bizarre in appearance or habits.
Traits:
Darkvision out to 60 feet and low-light vision.
Construct
A construct is an animated object or artificially constructed creature.
Traits:
No Constitution score.
No Good Saves
Darkvision out to 60 feet and low-light vision.
Immunity to all mind-affecting effects (charms, compulsions, phantasms, patterns, and morale effects).
Immunity to poison, sleep effects, paralysis, stunning, disease, death effects, and necromancy effects.
Cannot heal damage on their own, but often can be repaired by exposing them to a certain kind of effect (see the creature’s description for details) or through the use of the Craft Construct feat. A construct with the fast healing special quality still benefits from that quality.
Not subject to critical hits, nonlethal damage, ability damage, ability drain, fatigue, exhaustion, or energy drain.
Immunity to any effect that requires a Fortitude save (unless the effect also works on objects, or is harmless).
Not at risk of death from massive damage. Immediately destroyed when reduced to 0 hit points or less.
Since it was never alive, a construct cannot be raised or resurrected.
Because its body is a mass of unliving matter, a construct is hard to destroy. Resilient (+5 hp, +2 hp per hit die)
Constructs do not eat, sleep, or breathe.
Dragon
A dragon is a reptilelike creature, usually winged, with magical or unusual abilities.
Traits:
Darkvision out to 60 feet and low-light vision.
Immunity to magic sleep effects and paralysis effects.
Dragons are notoriously hard to kill. Resilient (+5 hp, +2 hp per hit die)
Elemental
An elemental is a being composed of one of the four classical elements: air, earth, fire, or water.
Traits:
Darkvision out to 60 feet.
Immunity to poison, sleep effects, paralysis, and stunning.
Not subject to critical hits or flanking.
Unlike most other living creatures, an elemental does not have a dual nature—its soul and body form one unit. When an elemental is slain, no soul is set loose. Spells that restore souls to their bodies, such as raise dead, reincarnate, and resurrection, don’t work on an elemental. It takes a different magical effect, such as limited wish, wish, miracle, or true resurrection, to restore it to life.
Elementals do not eat, sleep, or breathe.
Fey
A fey is a creature with supernatural abilities and connections to nature or to some other force or place. Fey are usually human-shaped.
Traits:
Low-light vision.
(Sprite)
Sprites are reclusive fey. They go out of their way to fight evil and ugliness and to protect their homelands.
Traits:
Frail (-5 hp, -2 hp per hd)
All sprites have a +2 racial bonus on Perception checks.
Humanoid
A humanoid usually has two arms, two legs, and one head, or a humanlike torso, arms, and a head. Humanoids have few or no supernatural or extraordinary abilities, but most can speak and usually have well-developed societies. They usually are Small or Medium. Every humanoid creature also has a subtype.
Humanoids with 1 Hit Die exchange the features of their humanoid Hit Die for the class features of a PC or NPC class.
Traits
Proficient with all simple weapons or by character class.
(Giant)
A giant is a humanoid of great strength, usually of at least Large size.
Traits:
Low-light vision.
Giants are tougher than even their great size would normally indicate. Tough (+3 hp, +1 hp per hit die)
(Goblinoid)
Goblinoids are stealthy humanoids who live by hunting and raiding and who all speak Goblin.
(Monstrous)
Monstrous humanoids are humanoids with monstrous or animalistic features. They often have magical abilities as well.
Traits:
Darkvision out to 60 feet
(Reptilian)
These humanoids are scaly and usually coldblooded.
Ooze
An ooze is an amorphous or mutable creature, usually mindless.
Traits:
Mindless: No Intelligence score, and immunity to all mind-affecting effects (charms, compulsions, phantasms, patterns, and morale effects).
Blind (but have the blindsight special quality), with immunity to gaze attacks, visual effects, illusions, and other attack forms that rely on sight.
Immunity to poison, sleep effects, paralysis, polymorph, and stunning.
Some oozes have the ability to deal acid damage to objects. In such a case, the amount of damage is equal to 10 + ½ ooze’s HD + ooze’s Con modifier per full round of contact.
Not subject to critical hits or flanking.
Oozes eat and breathe, but do not sleep.
Outsider
An outsider is at least partially composed of the essence (but not necessarily the material) of some plane other than the Material Plane. Some creatures start out as some other type and become outsiders when they attain a higher (or lower) state of spiritual existence.
Traits:
Darkvision out to 60 feet.
Unlike most other living creatures, an outsider does not have a dual nature—its soul and body form one unit. When an outsider is slain, no soul is set loose. Spells that restore souls to their bodies, such as raise dead, reincarnate, and resurrection, don’t work on an outsider. It takes a different magical effect, such as limited wish, wish, miracle, or true resurrection to restore it to life. An outsider with the native subtype can be raised, reincarnated, or resurrected just as other living creatures can be.
Proficient with all simple and martial weapons.
Outsiders breathe, but do not need to eat or sleep (although they can do so if they wish).
(Angel)
Angels are a race of celestials, or good outsiders, native to the good-aligned Outer Planes.
Traits:
Darkvision out to 60 feet and low-light vision.
Immunity to acid, cold, and petrification.
Resistance to electricity 10 and fire 10.
+4 racial bonus on saves against poison.
Protective Aura (Su): Against attacks made or effects created by evil creatures, this ability provides a +4 deflection bonus to AC and a +4 resistance bonus on saving throws to anyone within 20 feet of the angel. Otherwise, it functions as a magic circle against evil effect and a lesser globe of invulnerability, both with a radius of 20 feet (caster level equals angel’s HD). (The defensive benefits from the circle are not included in an angel’s statistics block.)
Tongues (Su): All angels can speak with any creature that has a language, as though using a tongues spell (caster level equal to angel’s Hit Dice). This ability is always active.
(Archon)
Archons are a race of celestials, or good outsiders, native to lawful good-aligned Outer Planes.
Traits
Darkvision out to 60 feet and low-light vision.
Aura of Menace (Su): A righteous aura surrounds archons that fight or get angry. Any hostile creature within a 20-foot radius of an archon must succeed on a Will save to resist its effects. The save DC varies with the type of archon, is Charisma-based, and includes a +2 racial bonus. Those who fail take a -2 penalty on attacks, AC, and saves for 24 hours or until they successfully hit the archon that generated the aura. A creature that has resisted or broken the effect cannot be affected again by the same archon’s aura for 24 hours.
Immunity to electricity and petrification.
+4 racial bonus on saves against poison.
Magic Circle against Evil (Su): A magic circle against evil effect always surrounds an archon (caster level equals the archon’s Hit Dice). (The defensive benefits from the circle are not included in an archon’s statistics block.)
Teleport (Su): Archons can use greater teleport at will, as the spell (caster level 14th), except that the creature can transport only itself and up to 50 pounds of objects.
Tongues (Su): All archons can speak with any creature that has a language, as though using a tongues spell (caster level 14th). This ability is always active.
(Demon)
Demons are a race of creatures native to chaotic evil-aligned Outer planes.
Traits
Immunity to electricity and poison.
Resistance to acid 10, cold 10, and fire 10.
Summon (Sp): Many demons share the ability to summon others of their kind (the success chance and type of demon summoned are noted in each monster description). Demons are often reluctant to use this power until in obvious peril or extreme circumstances.
Telepathy.
(Devil)
Devils are fiends from lawful evil-aligned Outer planes.
Traits
Immunity to fire and poison.
Resistance to acid 10 and cold 10.
See in Darkness (Su): Some devils can see perfectly in darkness of any kind, even that created by a deeper darkness spell.
Summon (Sp): Some devils share the ability to summon others of their kind (the success chance and type of devils summoned are noted in each monster description).
Telepathy.
(Eladrin)
Eladrins are a race of creatures native to the chaotic good-aligned Outer planes.
Darkvision out to 60 feet and low-light vision.
Immune to electricity and petrification.
Resistance to cold 10 and fire 10.
Tongues (Su): All eladrin can speak with any creature that has a language, as though using a tongues spell (caster level 14th). This ability is always active.
(Native)
Native outsiders have mortal ancestors or a strong connection to the Material Plane and can be raised, reincarnated, or resurrected just as other living creatures can be.
Traits:
May be be raised, reincarnated, or resurrected by spells that restore souls to their bodies, such as raise dead, reincarnate, and resurrection.
Native outsiders breathe, eat, and sleep.
Plant
This type comprises vegetable creatures. Note that regular plants, such as one finds growing in gardens and fields, lack Wisdom and Charisma scores (see Nonabilities) and are not creatures, but objects, even though they are alive.
Traits:
Low-light vision.
Immunity to all mind-affecting effects (charms, compulsions, phantasms, patterns, and morale effects).
Immunity to poison, sleep effects, paralysis, polymorph, and stunning.
Not subject to critical hits.
Plants breathe and eat, but do not sleep.
Vermin
Vermin include insects, arachnids, other arthropods, worms, and similar invertebrates.
Traits:
Mindless: No Intelligence score, and immunity to all mind-affecting effects (charms, compulsions, phantasms, patterns, and morale effects).
Darkvision out to 60 feet.
(Air)
This subtype usually is used for elementals and outsiders with a connection to the Elemental Plane Air. Air creatures always have fly speeds and usually have perfect maneuverability.
(Aquatic)
These creatures always have swim speeds and thus can move in water without making Swim checks. An aquatic creature can breathe underwater. It cannot also breathe air unless it has the amphibious special quality.
(Chaotic)
A subtype usually applied only to outsiders native to the chaotic-aligned Outer Planes. Most creatures that have this subtype also have chaotic alignments; however, if their alignments change they still retain the subtype. Any effect that depends on alignment affects a creature with this subtype as if the creature has a chaotic alignment, no matter what its alignment actually is. The creature also suffers effects according to its actual alignment. A creature with the chaotic subtype overcomes damage reduction as if its natural weapons and any weapons it wields were chaotic-aligned.
(Cold)
A creature with the cold subtype has immunity to cold. It has vulnerability to fire, which means it takes half again as much (+50%) damage as normal from fire, regardless of whether a saving throw is allowed, or if the save is a success or failure.
(Dire)
Dire creatures are larger, tougher, meaner versions of their type. Each kind tends to have a feral, prehistoric, or even demonic appearance.
Traits:
Tough (+3 hp, +1 hp per hd)
Feral (+2 bonus on attack rolls made using natural weapons)
(Earth)
This subtype usually is used for elementals and outsiders with a connection to the Elemental Plane of Earth. Earth creatures usually have burrow speeds, and most earth creatures can burrow through solid rock.
(Extraplanar)
A subtype applied to any creature when it is on a plane other than its native plane. A creature that travels the planes can gain or lose this subtype as it goes from plane to plane. Monster entries assume that encounters with creatures take place on the Material Plane, and every creature whose native plane is not the Material Plane has the extraplanar subtype (but would not have when on its home plane). Every extraplanar creature in this book has a home plane mentioned in its description. Creatures not labeled as extraplanar are natives of the Material Plane, and they gain the extraplanar subtype if they leave the Material Plane. No creature has the extraplanar subtype when it is on a transitive plane, such as the Astral Plane, the Ethereal Plane, and the Plane of Shadow.
(Evil)
A subtype usually applied only to outsiders native to the evil-aligned Outer Planes. Evil outsiders are also called fiends. Most creatures that have this subtype also have evil alignments; however, if their alignments change, they still retain the subtype. Any effect that depends on alignment affects a creature with this subtype as if the creature has an evil alignment, no matter what its alignment actually is. The creature also suffers effects according to its actual alignment. A creature with the evil subtype overcomes damage reduction as if its natural weapons and any weapons it wields were evil-aligned.
(Fire)
A creature with the fire subtype has immunity to fire. It has vulnerability to cold, which means it takes half again as much (+50%) damage as normal from cold, regardless of whether a saving throw is allowed, or if the save is a success or failure.
(Good)
A subtype usually applied only to outsiders native to the good-aligned Outer Planes. Most creatures that have this subtype also have good alignments; however, if their alignments change, they still retain the subtype. Any effect that depends on alignment affects a creature with this subtype as if the creature has a good alignment, no matter what its alignment actually is. The creature also suffers effects according to its actual alignment. A creature with the good subtype overcomes damage reduction as if its natural weapons and any weapons it wields were good-aligned.
(Incorporeal)
Traits:
No physical body: Incorporeal creatures can be harmed only by other incorporeal creatures, magic weapons or creatures that strike as magic weapons, and spells, spell-like abilities, or supernatural abilities. It is immune to all nonmagical attack forms. Even when hit by spells or magic weapons, it has a 50% chance to ignore any damage from a corporeal source (except for positive energy, negative energy, force effects such as magic missile, or attacks made with ghost touch weapons). Although it is not a magical attack, holy water can affect incorporeal undead, but a hit with holy water has a 50% chance of not affecting an incorporeal creature.
Incorporeal creatures can enter or pass through solid objects, but must remain adjacent to the object’s exterior, and so cannot pass entirely through an object whose space is larger than its own. It can sense the presence of creatures or objects within a square adjacent to its current location, but enemies have total concealment (50% miss chance) from an incorporeal creature that is inside an object. In order to see farther from the object it is in and attack normally, the incorporeal creature must emerge. An incorporeal creature inside an object has total cover, but when it attacks a creature outside the object it only has cover, so a creature outside with a readied action could strike at it as it attacks. An incorporeal creature cannot pass through a force effect.
Incorporeal creatures pass through and operate in water as easily as they do in air.
Incorporeal creatures have no weight and do not set off traps that are triggered by weight.
Incorporeal creatures cannot fall or take falling damage.
Nonvisual senses, such as scent and blindsight, are either ineffective or only partly effective with regard to incorporeal creatures.
Incorporeal creatures have an innate sense of direction and can move at full speed even when they cannot see.
An incorporeal creature moves silently and cannot be heard with Listen checks if it doesn’t wish to be.
Deflection: Incorporeal creatures have no natural armor bonus but have a deflection bonus equal to their Charisma bonus (always at least +1, even if the creature’s Charisma score does not normally provide a bonus).
Touch Attacks: An incorporeal creature’s attacks are touch attacks, as they pass through natural armor, armor, and shields. It has no Strength score, so its Dexterity modifier applies to both its melee attacks and its ranged attacks.
Incorporeal creatures cannot make trip or grapple attacks, nor can they be tripped or grappled. In fact, they cannot take any physical action that would move or manipulate an opponent or its equipment, nor are they subject to such actions.
(Lawful)
A subtype usually applied only to outsiders native to the lawful-aligned Outer Planes. Most creatures that have this subtype also have lawful alignments; however, if their alignments change, they still retain the subtype. Any effect that depends on alignment affects a creature with this subtype as if the creature has a lawful alignment, no matter what its alignment actually is. The creature also suffers effects according to its actual alignment. A creature with the lawful subtype overcomes damage reduction as if its natural weapons and any weapons it wields were lawful-aligned.
(Shapechanger)
A shapechanger has the supernatural ability to assume one or more alternate forms. Many magical effects allow some kind of shape shifting, and not every creature that can change shape has the shapechanger subtype.
(Water)
This subtype usually is used for elementals and outsiders with a connection to the Elemental Plane of Water. Creatures with the water subtype always have swim speeds and can move in water without making Swim checks. A water creature can breathe underwater and usually can breathe air as well.
(Undead)
Undead are once-living creatures animated by spiritual or supernatural forces.
Traits:
No Constitution score.
Darkvision out to 60 feet.
Immunity to all mind-affecting effects (charms, compulsions, phantasms, patterns, and morale effects).
Immunity to poison, sleep effects, paralysis, stunning, disease, and death effects.
Not subject to critical hits, nonlethal damage, ability drain, or energy drain. Immune to damage to its physical ability scores (Strength, Dexterity, and Constitution), as well as to fatigue and exhaustion effects.
Cannot heal damage on its own if it has no Intelligence score, although it can be healed. Negative energy (such as an inflict spell) can heal undead creatures. The fast healing special quality works regardless of the creature’s Intelligence score.
Immunity to any effect that requires a Fortitude save (unless the effect also works on objects or is harmless).
Not at risk of death from massive damage, but when reduced to 0 hit points or less, it is immediately destroyed.
Not affected by raise dead and reincarnate spells or abilities. Resurrection and true resurrection can affect undead creatures. These spells turn undead creatures back into the living creatures they were before becoming undead.
Undead do not breathe, eat, or sleep.
Ok, now that all of that is out of the way, a few examples of why I'm going to all this trouble. Here's the rewritten Dire Tiger, it's basic melee combat abilities remain mostly unchanged, but it no longer has the ridiculously high will and reflex saves of the SRD version. The SRD version had Ref +12, Will +11, if you're wondering. The Reflex save was forgivable, but a non-intelligent animal having a will save 4-6 points higher than even caster type enemies at it's CR was just silly.
Dire Tiger
Large Animal (Dire) [Assault]
HD: 8d10+75 (119 hp)
Initiative: +2
Speed: 40 ft. (8 squares)
Armor Class: 17 (-1 size, +2 dex, +6 Natural), touch 11, flat-footed 15
Base Attack: +8
CMB: +17
Attack: Claw +18 melee (2d4+8)
Full Attack: 2 claws +18 melee (2d4+8) and bite +12 melee (2d6+4)
Space/Reach: 10 ft./5 ft.
Special Attacks: Improved grab, pounce, rake 2d4+4
Special Qualities: Feral, low-light vision, scent, tough
Saves: Fort +14, Ref +8, Will +3
Abilities: Str 27, Dex 15, Con 26, Int 2, Wis 12, Cha 10
Skills: Perception +8, Stealth +9*
Feats: Improved Natural Attack (claw), Improved Natural Attack (bite), Weapon Focus (claw), Run
Environment: Warm forests
Organization: Solitary or pair
Treasure: None
Alignment: Always Neutral
Improved Grab (Ex)
To use this ability, a dire tiger must hit with its bite attack. It can then attempt to start a grapple as a free action without provoking an attack of opportunity. If it wins the grapple check, it establishes a hold and can rake.
Pounce (Ex)
If a dire tiger charges, it can make a full attack, including two rake attacks.
Rake (Ex)
Attack bonus +18 melee, damage 2d4+4.
Feral
Dire Tigers receive a +2 bonus to attacks made with natural weapons.
Tough
Dire animals are abnormally tough, giving them +3 bonus hp, and an additional +1 bonus hp per hit die.
Skills
Dire tigers have a +4 racial bonus on stealth checks. *In areas of tall grass or heavy undergrowth, the Hide bonus improves to +8.