One difficulty I had with 3.x was that flat-bonus feats (such as Skill Focus and Weapon Specialization) did not scale with level. This meant that, while they may be useful at an early point in the game, or as prerequisites for other things (PrCs, feats), they were less impressive as time went on.
For example, Weapon Focus. At 1st level, the +1 to strike is useful, if you have your chosen weapon. While subsequent levels would allow you to take Improved, Greater, and Weapon Focus with a Cherry on Top, these required further investments in resources, making the initial feat a sub-optimal investment... it was a gateway to greater bonuses, but only if you were willing to buy into the pyramid.
I have suggested that these feats should provide a static bonus, plus an additional bonus every X levels; weapon focus, for example, providing a +1 at level 1, and an additional +1 at levels 4, 8, 12, 16 and 20, keeping a focused character with a 3/4 BAB equal in bonus to a non-focused character with a 1/1 BAB, but without the benefits of improved BAB. Skill focus would be +2 at first level, and an additional +1 every third level, making for a useful bonus, instead of a static brick around your prestige-classed neck.