I think the biggest element added to 3E that was a bad decision was the implementation of Prestige Classes.
Virtually all PrCs have either more utility or more power than the same level base class. Because of this, the proliferation of splat books was almost a requirement for the game (i.e. a player does not want to buy a splat book and then be told that he cannot play his favorite PrC out of that book).
The prerequisites for PrCs also added a major element of designing a PC for the future, not for the present.
I like the concept of PrCs, but I think that they should be slightly weaker than base classes and have virtually no special prerequisites. Not significantly weaker, but slightly.
That way, the incentive for taking a PrC is for flavor and roleplaying reasons, not soley for crunch power reasons.
In 3E/3.5, many players will say that they that they want a specific PrC for flavor or roleplaying reasons, but I suspect that it is also for crunch power reasons as well most of the time. Why have a Sorcerer above 10th level if virtually nobody ever takes it?
I hope they fix this for 4E, but I haven't yet seen anything that indicates that they even perceive a problem here.