Prestige Classes, for example. Particularly, when you started getting two or three front loaded classes that allowed you to play what was already a viable concept, but better, and then you started people charop's by just assuming they could enter into two or three prestige classes.
Increased spell lists for another, particularly because there was nothing balancing divine casters. Every single spell published became an available class feature.
Indeed, just about everything introduced in 3.5 actively harmed the game. Playtesting was non-existent. The publishing schedule was everything. Every book had to offer new chargen options because they were wanting to drive sales by making sure the book would appeal to both players and GMs. So every book was just lousy with new chargen options. No game requires 600 prestige classes, and if yours does, something is wrong with the game. What's worse, aside from the Pun-Pun problem and needing table agreements as to how much you were going to break the game, is that with all those chargen options, tons of archetypal characters still weren't really playable. Because invariably, to meet deadlines everyone would just go after the easiest concepts and the lowest hanging fruit.
Complete mess. 3.5e was too compatible with 3.0e to actually fix any of its problems, so instead it just buried the problems under a mountain of other problems.