What's wrong with D&D 3.5? There is a short answer and a long answer. The short answer is that it is far too complicated. From top to bottom, there are too many rules and too many special cases. The rules for feats and skills and combats are the ones that bother me the most, but each is deserving of it's own post.
The special cases are what drives me insane. It seems that every section in the combat chapter states a rule, how it works, exactly what it entails, provides an example
and then lists a feat(s) that modify how that rule works. This reminds me of the old game system/setting Earthdawn, where characters would acquire powers, very similar to feats, as they increased in experience. It makes life for a Game Master difficult on two levels. First, it increases adventure design time exponentially, especially at higher levels when you must assign massive numbers of skill points and select a dozen feats for each NPC. If you earn your living writing modules for pay, no problem. However, this is far too much paperwork for a hobby! I'm lucky to have any time left over for character motivations or plot hooks and twists.
Second, all of the special cases make combat slow down to a crawl, between players trying to plot out their character's movement without incurring an attack of opportunity, or choosing from their laundry list of skills, or scanning through their player's handbook trying to figure out how x feat will react when combined with skill y against class ability z! It's a pure nightmare! Especially when everyone pauses from the action to look up a particular rule or feat! It's a focus killer, par excellence!