Counterspells. The counterspell mechanic, as it currently stands, is useless. You have to ready an action to cast the exact same spell... and with the abundance of spells in D&D, that's not going to happen.
Unless you burn a feat. And then, you waste a spell slot so that you can deny your opponent a chance to act. Which is, I guess, okay... if the PHB as written used immediate actions.
Trained-only skills! If a character has no ranks in a skill, they're probably not going to succeed on a roll of any import, but they should at least be able to try. Why can someone Jump without training, but not Tumble?
No rule actually says you cannot tumble without ranks... you just don't get the benefit of avoiding the AoO
BTW, in the list so far, the only rule which I really don't like is grappling which is way too complicated.
All other nominations are not bad rules for my taste.
Allow me to add some hate towards the Spiked Chain and Fixed Save DC's. The former because it is the Paris Hilton of weapons; dumb and pointless yet everyone keeps talking about it.