Counting just WotC and Paizo, there are well over 2,500 unique published feats for various purposes. The count is over 3,000 if you count duplicate printings. My complaints about how they have been handled include the following.
1) Too many feats are listed as "General." A feat that increases spell DC, one that changes attacks of opportunity, and one that increases land movement are all considered the same type of feat.
2) It should be easier to tell which feats I'm not interested in right now. What I mean is that a LOT of feats require a specific race, class ability, campaign background or can only be taken at first level. That should be clearly visible and not buried in the prerequisites. The Warforged and Shifter feats in Eberron do a good job of this.
3) There are a handful of feats, like Saddleback, that appear in a whole bunch of different campaign settings with prerequisities that are setting-dependent. It would be nice to have more consistency in how this is expressed. Now, these could be listed as Regional, Ancestor, Racial, or General feats, depending on the predelictions of the author.
4) It would be nice to see some guidelines on what should be considered a potential fighter, monk, or wizard bonus feat, since the published materials are sometimes inconsistent on which are bonus feats and which are not. For example, any feat that affects attack rolls, combat damage, proficiency, armor class, initiative, or attacks of opportunity that does not involve abilities a human fighter would not have should be considered a fighter bonus feat, with the DM being the final judge.
5) There are some very deep feat trees for doing things like shield bashing. I would prefer more generic feats. A light shield is considered a light weapon in 3.5 if it is used to bash, so why do we need a whole host of separate feats to give it extra capabilities?
Anyway, just some thoughts.