Power-wise, natural spell is my #1 problem, mainly because it is core and I have to house rule it.
For clunky implementation, 3.5's power attack wins: with 2 for 1 for some weapons and 0-for-1 for others versus 3.0's very simple formula. I end up house ruling that one too.
For mere annoyance, dodge is very annoying because having to declare your dodge on a individual combatant is too much minutia for the game. And as a DM, I never remember to check the Feat line of a monster to find out if he has dodge or not.
Non-core, I don't like 3.0's spellcasting prodigy for power reasons. But then I don't allow many non-core feats into my game.