Here's some examples of how fighters should interact with feats.
Shield Focus: When using a Shield, the AC bonus granted by the shield increases by +1.
Fighters: a Fighter may trade his Tower Shield Proficiency for this feat at first level.
Shield Slam: YOu may make a bull rush attempt for free if you hit someone with a shield slam. Req: Shield Focus
Fighter: You are treated as if you have the TWF skill when using a shield. This improves up the TWF tree as your BAB improves and grants additional attacks, but only for shields.
You are treated as if shields are part of your Weapon Mastery if they are wielded along with weapons in those groups.
At Fighter level 6, you gain Shield Mastery (enhance bonus is defense + offense) and you take no penalties on your primary weapon when fighting with a shield while Shield Bashing.
If you declare TWF with a shield, you may add the str bonus on your shield arm to your primary weapon, instead of using it on the shield bash, if you so choose (i.e. +1/2 Str).
If you have Dodge or Lightning Reflexes, you may add your Shield AC bonus to all Reflex saves.
If you have Missile Deflection, you may use a shield to deflect missiles (adding its enhancement bonus to the roll), and may apply your Shield Bonus against touch attacks and ranged touch attacks.
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Dodge: You gain a +1 Dodge bonus to AC. Req: Dex 13
Fighter: You ignore the Dex req. Your Armor Training bonus becomes a Dodge bonus to AC, and a bonus to Reflex saves. It no longer increases the Dex limit of your armor, but still reduces the Armor Check penalty.
And for the classic:
Weapon Focus: +1 to hit with a weapon.
Fighters: Weapon Specialization: The bonuses with the weapon are equal to your highest class weapon training bonus.
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Iron Will: +2 to Will saves.
Fighters: You also add your Bravery bonus to all Will saves. You may immediately reroll a failed Will save once a day if you fail it, with a +2 bonus on the roll.
Ditto Lightning Reflexes and Great Fortitude, for Armor Training and Weapon Training respectively.
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Expertise: subtract Th for AC. Int Req: 13
Fighters: A fighter may ignore the Intelligence requirement.
A fighter may choose one saving throw to add a morale bonus equal to his AC bonus to when using Expertise.
If the fighter has a Defending Weapon with his Weapon Specialization, he may use the Defender property whenever he is using Expertise (i.e. he is not required to be attacking in melee).
When using Defensive Fighting, the fighter's BAB subs for the Acrobatic requirements for improved benefits.
A fighter adds his Expertise benefit when performing a Feint, or attempting to see through a Feint, and to his CMD, at all times.
Pick a knowledge based skill. That skill is now a Fighter class skill for you.
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Skill Affinity: Pick two skills. You gain +2 in those skills, improving to +4 at 10th.
Skill Focus: +3, improving to +6 in one skill.
Fighter: The skills chosen become class skills for your fighter levels. Wis and Cha skills so chosen gain a morale bonus equal to your Bravery bonus. Str and Con skills gain a morale bonus equal to your highest Weapon Training bonus. Int and Dex skills gain a morale bonus equal to your Armor Training bonus.
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Fighter core skills all fighters should have: Jump, Perception, Knowledge (martial/military/nobility), Intimidate. THeir fighter levels should sub for Acrobatics for Defensive fighting, for Bluff when Feinting, and for Sense Motive against Feints.
Intimidate: Fighters subtract their Fighter level from attempts to Intimidate them, as long as they have Intimidate ranks at least equal to their level.
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Inert: Req: No magical ability, period. This includes rage rounds, ki pools, nature's bond, and other supernatural powers.
You gain SR against hostile spell effects equal to your BAB + Fort Save. IF you have the evasion class feature, you may instead use your Reflex save.
Renaissance fighter: At first level, a fighter may trade his heavy and medium armor proficiencies for +1 Skill points/level and 1 additional class skill of his choice, each.
Duelist trained: At first level, the fighter may take weapon finesse as a bonus feat. He loses proficiency in all non-finessable martial weapons.
Toughness: |+3 hp, or +1 hp/level, whichever is higher.
Fighter: You gain 1 temp hp/fighter level at the beginning of each round, as long as you are above 0 hit points. Damage taken each round comes from these temporary hit points first. These hit points work for only one round against continuous damage effects, such as being grappled or area environmental damage. They are renewed at the beginning of each round.
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Why isn't this done normally when it's so obvious?
Because it turns fighters into spellcasters, and forces the entire feat section of the book, which is supposed to nominally be equal for all characters, into basically another fighter-centric spell list.
Can't have that, now, can we?
==Aelryinth
Here's a goofball feat to reflect the power of Extra Rage Power, etc:
Improved Saves: If taken as a Fighter combat feat, you may select either two skill feats or two saving throw feats instead of a fighter bonus combat feat.
Double powered feats for the price of one!...
==Aelryinth
Two weapon Fighting:
Fighters: This automatically improves to Improved and Greater at the appropriate levels.
Fighters ignore the Dexterity requirement of the feat.
When TWF, your weapons automatically gain your Weapon Mastery and Weapon Specialization on both weapons if either weapon is trained in them.
If you have the Expertise feat, you gain a +1 Shield bonus when TWF.
==Aelryinth
We all know how much Vital Strike sucks.
Here's my take on trying to make it (more) viable.
Vital Strike you have to be careful of. the reason is that if you get to include all bonuses in the multiplier, it both does more damage then a full attack does, AND you get to move.
So, a Vital Strike should deal less damage then a full attack, simply because it allows some movement.
Also, it should be viable from level 1.
Vital Strike: BAB +6 You do double the normal weapon damage with a single standard action attack.
Fighters: No Requirements. You gain the following option: You may take a full attack action to deal a single Vital Strike, and gain either +2 to hit or AC. This improves by +1 for each additional iterative attack you have. (Note: this works perfectly fine at level 1).
You may include your Weapon Training and Weapon Spec bonuses when multiplying damage on a vital strike (used because these are static, fixed bonuses directly derived from your class).
If you attack in combat using a Quick Draw and Vital Strike against an adjacent opponent, he is considered flat-footed against the attack. You may only do this once per combat.
If you have the Whirlwind, Spring Attack, or Cleave feats, you may use a Vital Strike with them (extra damage applies only to the first attack).
If you have BAB 6+, you may use a Vital Strike on a charge.
At Fighter levels 6,11, and 16, your Vital Strike improves to the next feat level category (x2, x3 and x4 damage, respectively).
If you have the expertise feat, your Vital Strike cannot be parried or annulled (by Crane Wing, etc).
==Aelryinth
For what it's worth, and for those who haven't seen them a million times, click on Chapter 5 for my approach to feats. Aylerinth is familiar with them, and indeed seems to be taking a simular approach with many of his suggestions.