This thread is mostly in response to this thread which touches heavily on issues with alignments, positive/negative energy, many creatures including most undead, and the effects of several spells. These are some of the modifications I made to the system in my own games (pre-Pathfinder) and I think they would work very well for the Pathfinder RPG.
I declare all of this open source and my gift to Paizo for their hard work, and their continuing to impress me on a constant basis (and soon, all of those pathfinder paths, with be mine and with a subscription to boot).
--==Introduction==--
There are many inconsistencies, contradictions, and problematic troubles with the 3.5 System Reference Document's materials; especially when it pertains to matters such as alignment effects, alignment subtypes (for spells), the effects of some spells which directly make use of these aspects of the game, and finally, the representation of positive and negative energies in the SRD.
It would seem that the writers responsible for writing 3.5 (including the revisions from 3.0) had differing views on these subjects, and how each interacted with one-another throughout the entire system. They also seem to have made alternations to the 3.0 system which were poorly thought out (which will be discussed in my notes at the end of this post). The goals of this post are simple - 1) To remove some internal conflicts within the core system, 2) to make the system less campaign-specific, and a more fluid system usable for a wider variety of individual games.
Now let's get started!
--==Creature Alignment and Subtypes==--
A mindless creature without an intelligence score always has an alignment of Neutral. Creatures and animate objects without an intelligence score cannot have a moral alignment other than Neutral regardless of their origins. Alter creatures such as Skeletons, Zombies, Lemures, and other mindless creatures' alignments to Neutral.
If a creature is innately born of a certain alignment such as Lemures which are formed out of raw evil, and are mindless lesser devils, will have the [Evil] creature subtype, effectively making them subject to any effects which rely on alignment (such as spells like Holy Smite, Smite Evil, Holy Word, Protection from Evil and so forth).
(-Notes-: This is a much more elegant way of dealing with mindless creatures needing alignments to allow them to be affected by certain abilities, and it also cements the idea that such creatures are wholly evil because of their nature.)
--==Spell Alterations==--
The following spells should be altered to fit and interact within the system more appropriately.
Detect Evil
As per SRD but replace Undead with "Evil Subtype".
Consecrate
As per the SRD but change the spell name to Positive Energy Well. Alter the bonus on turning checks to affect the channel energy DC for positive energy channeling, and change the type of bonus to +3 competence.
Optional: Alter the material component to be a pearl worth 25 gold pieces, instead of 25gp holy water.
Desecrate
As per the SRD but change the spell name to Negative Energy Well. Alter the penalty for turn undead into a +3 competence bonus to the DC of channel negative energy.
Optional: Alter the material component to be a jet stone worth 25 gold pieces, instead of 25gp unholy water.
Hallow
As per SRD but change the modifiers to turn and rebuke undead to instead change the DC for channel positive energy, and channel negative energy respectively, and change the type to competence.
Unhallow
As per SRD but change the modifiers to turn and rebuke undead to instead change the DC for channel positive energy, and channel negative energy respectively, and change the type to competence.
Animate Dead
As per SRD but remove the [Evil] descriptor.
Add the line "skeletons and zombies continue to preform their last order until completed or until their destruction".
Optional: Add the following text at the end of animate dead.
You may create skeletons and zombies with the [Evil] subtype, creating Vile Undead. These undead are stronger than standard skeletons and zombies, having special abilities powered by raw evil power. When uncontrolled, they attack and kill any living thing they come in contact with until control is regained or they are destroyed. If cast in this way, Animate Dead gains the [Evil] spell descriptor.
--==Clerics and Channel Energy==--
Give clerics (both good and evil) the option of channeling positive or negative energy (and spontaneously casting cure or inflict spells respectively), regardless of the clerics alignment. This will allow greater customization and options with the class (with offensive warrior clerics of good having access to a new weapon, and giving evil clerics a better option to fight undead or heal allies - as well as give the option for good undead to channel negative energy, and evil undead to channel positive energy to harm other undead).
--==Optional: Sample Vile Undead==--
When making vile undead, you really only need to add the [Evil] descriptor to the undead in question; however, some DMs may wish to make particularly nasty undead which have a number of evil resistances or powers. These are slightly more powerful than typical undead of their kind, and may not be suitable for every campaign.
Vile undead are identical to regular undead, however each has some sort of unholy ability gained through its evil infused existence. Vile Undead is a template that can be added to any undead creature (hereafter referred to as the "base creature").
Size and Type: Size remains the same. Add [Evil] subtype.
Special Qualities: The base creature retains any special qualities it had before, and gains the ones listed below.
Infernal Vigor: The base creature gains +1 hit point per hit dice.
Violence: The base creature gains a +1 profane bonus on attack and +2 on damage rolls with any natural or manufactured weapon attacks made against good or neutral creatures.
Abyssal Armor: The base creature gains DR 1/Good for every two hit dice of the base creature (minimum DR of 1/Good).
CR: As base creature +1
Level Adjustment: +1
Sample Vile Undead
Vile Human Warrior Skeleton
Size and Type: Medium Undead [Evil]
Hit Dice: 1d12+1 (7hp)
Initiative: +5
Speed: 30ft
Armor Class: 15 (+1 dex, +2 natural, +2 heavy steel shield), touch 11, flat-footed 14
Base Attack / CMB: +0/+1
Attack: Scimitar +2 melee (1d6+3, 18-20/x2) or claw +2 (1d4+3)
Full Attack: Scimitar +2 melee (1d6+3, 18-20/x2) or 2 claws +2 (1d4+3)
Space/Reach: 5ft./5ft
Special Attacks: _
Special Qualities: Damage reduction 5/bludgeoning, damage reduction 1/good, darkvision 60 ft., immunity to cold, undead traits, violence, infernal vigor
Saves: Fort +0, Ref +1, Will +2
Abilities: Str 13, Dex 13, Con Ø, Int Ø, Wis 10, Cha 1
Feats: Improved Initiative
Environment: Temperate Plains
Organization: Any
Challenge Rating: 1
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OK! That's enough.
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Ok, so here we go. That's more or less the extent of the changes I would suggest, and anything I've written here may be used by anyone anywhere. I've been using these in my games and it really helps things a lot. If I wish to run a game where morality is black and white, or undead are all inherently evil, I simply use [Evil] versions of them. However, the standard is neutral, and thus open to far more options.
Hope this is enjoyed by someone.
More work to come, perhaps.
Peace out, Game on.