Actually, I'm more inclined to say that there are too many feats in the 3.5E PHB:
1. All the skill bonus feats should be combined, and preferably made generic. (4 skill points, distribute how you like) Combat Casting and Endurance should be handled in this manner (get rid of Endurance per se, it's a weak feat).
2. There are too many item creation feats. In AD&D, any Wizard with Enchant an Item could make magic items. Reduce the number of item creation feats and simplify the system. I'd go for something like Monte Cook's Arcane Unearthed system: Craft Single-Use Item (Scroll, Potion, some Wondrous items), Craft Charged Item (Staff, Wand), Craft Constant Item (power in constant effect or activated (no charges), and weapons and armor). This frees up some feats for enchanters to be more than just flavorless enchanters.
3. Get rid of Combat Expertise. Make this a standard rule that anyone in combat can use.
4. Get rid of Mobility, or get rid of Tumble affecting combat. They overlap - should only have one of them.
5. Combine Cleave and Great Cleave. Cleave is good vs. mooks, but Great Cleave is useful even less often.
6. Get rid of Rapid Shot and Manyshot. They break standard mechanics for combat and can be too good in some circumstances (especially with Improved Rapid Shot).
7. Replace Power Attack by a feat that gives say +2 damage with two-handed weapons. Power Attack has complicated mechanics, and is often used at the wrong time by people who aren't familiar with the math behind it. i.e. Simplify.
8. Get rid of Improved Shield Bash. See more comments on Two-Weapon Fighting below.
9. Combine Spell Focus and Greater Spell Focus to give a flat +2 save DC for a magic school.
10. Get rid of Track. Allow anyone with Survival to track all DCs. Increase DC on tracking if you like, and give Rangers a bonus (e.g. +4 by 20th level).
11. Make Two-Weapon Fighting work like using Two-Handed weapons. For details see:
http://www.ucc.gu.uwa.edu.au/~knight/campaign/3edition/twoweapon.html
I would get rid of Greater Two Weapon Parry, but allow a Defender secondary weapon to add to AC. (Improved Shield Bash is now redundant - you use the shield as a shield, or as a secondary weapon to add to damage, but not both.)
12. Get rid of Weapon Finesse. Allow everyone to have Weapon Finesse. If your DEX bonus is higher than your STR bonus, it applies to attacks with light weapons, Rapier, spiked chain, and whip.
13. Some of the metamagic feats are quite weak. Allow everyone to use Heighten Spell by default (no feat needed) - i.e. use a higher level slot, and the spell DC increases. Combine Enlarge Spell, Extend Spell and Widen Spell into one feat (Modify Spell): rules stay the same, just makes the feat more useful, e.g. +2 levels for an extended, enlarged spell.
14. Get rid of Improved Grapple. Grappling provokes an attack of opportunity, and damage from that attack of opportunity penalizes (but does not prevent) your grapple attempt. Similarly, I'd probably get rid of Improved Disarm, Improved Trip, Improved Bull Rush, Improved Overrun, and Improved Sunder.
Now the other major change I would make, would be to make some class features generic feats. This could be done with a number of the class features. Classes then get bonus feats instead of these class features, so that they have more choice in feats.
1. As Mone Cook did in Arcana Unearthed, I'd make Uncanny Dodge and Improved Uncanny Dodge feats.
2. Increased Move +10' enchancement bonus in light or no armour and not encumbered as a feat, and this replaces the Run feat - i.e. let anyone add their DEX bonus to dodging when running. (I wouldn't give Monks too many bonus feats to replace this.)
Major changes, but I think it would simplify the feat system. Moreover, I don't want a whole lot of feats from other sources - many are too weak or too powerful. I would probably replace Toughness with Improved Toughness from Combat and Tactics (but only allow you to take Improved Toughness once). I would allow the Energy Substitution feat, but not with Sonic Energy.
This simplifies the number of choices characters need to make, and leaves the most useful feats in place. The weaker feats have mostly been removed. Characters generally have too few feats and too many feats that they want to take, so fewer feats reduces this issue slightly.
Just my (complicated) thoughts ...