One idea I've ben toying with, but never got round to giving it a complete write-up, is to make the effectiveness of the fighter feats dependant on the number of fighter feats that you have.
Given that a fighter gets 11 bonus feats from class levels by 20th level, and 7 more from character levels (8 if he is human), this means an absolute cap of 18 or 19 feats by level 20.
So, Weapon Focus could give a +1 bonus to attack rolls with the specified weapon, +1 for every 9 fighter feats you have, so a fighter that really focuses on fighting could get +3 to hit by 20th level. There would be no need for Greater Weapon Focus.
Weapon Specialization could apply to any weapon a character has taken Weapon Focus in, as suggested by sfedi, and could add +1 per 3 fighter feats to the damage dealt by that weapon, so a focused fighter could get +6 to damage by 20th level. Again, there would be no need for Greater Weapon Specialization.
The bonus for Improved Initiative, Improved Disarm, Improved Sunder, Improved Trip and similar feats could be 4 plus 1 per 4 fighter feats, so a high-level fighter could get a +8 bonus.
I'd make Combat Expertise work off fighting defensively, so that when fighting defensively, the penalty to attack rolls is only -2 (instead of -4). In addition, you get a +1 dodge bonus to AC for every 6 fighter feats that you have. So, a high-level fighter could take a -2 penalty to hit and get a +5 dodge bonus to AC.
Similarly, for Power Attack, you only take a -2 penalty to hit, and the bonus to damage depends on the weapon: A light weapon gets a +1 bonus to damage, +1 for every 9 fighter feats. A weapon used in one hand that is not light gets a +2 bonus to damage, +1 for every 6 fighter feats. A weapon used in two hands gets a +3 bonus to damage, +1 for every 3 fighter feats. A weapon used with Weapon Finesse is treated as one category lighter, so a rapier used with Weapon Finesse deals extra damage as a light weapon, and a spiked chain used with Weapon Finesse deals extra damage as a one weapon used in one hand. A barbarian can add the number of times he can rage per day to the number of fighter feats that he has to determine the effectiveness of this feat.
With Toughness, you get 2 hit points +1 for every fighter feat (including Toughness). This means that you can no longer take it multiple times, though.
Dodge gives you a +1 dodge bonus, +1 for every 9 fighter feats.
Improved Critical improves the threat range depending on the weapon. A weapon with a threat range of 20 improves its threat range by 1 plus 1 for every 18 fighter feats. A weapon with a threat range of 19-20 improves its threat range by 2 plus 1 for every 9 fighter feats. A weapon with a threat range of 18-20 improves its threat range by 3 plus 1 for every 6 fighter feats. In addition, it would apply to any weapon a character has taken Weapon Focus in.
Cleave can be used once per round, plus an additional time for every 3 fighter feats. There would be no need for Great Cleave.
Improved Unarmed Strike could increase the base damage of your unarmed strikes by one step per 3 fighter feats. A monk can add his monk level to his number of fighter feats to determine the effectiveness of this feat.
Deflect Arrows could allow you to deflect one arrow per round, plus an additional arrow for every 9 fighter feats. A monk can add his monk level to his number of fighter feats to determine the effectiveness of this feat.
Stunning Fist could be used once per day, plus once more per two fighter feats. A monk can add his monk level to his number of fighter feats to determine the effectiveness of this feat.
Thoughts? Other suggsestions?