The spiked chain. IME, this thing is just a game killer. Once you have a spiked chain fighter on the loose, any other melee specialists are hosed. To keep the chain fighter challenged, you have to take a ton of care to sculpt opponents to threaten him. Otherwise, the game gets dumb.
The chain had a perfect storm of changes that all made it better - Power Attack 2/1 damage, the change to Improved Disarm, the change to Improved Trip, and the new rules for reach for Large and bigger creatures all make it too good. The annoying thing is I can see how, on their own, those changes make sense, but combined into the spiked chain it's too much.
On the plus side, it illustrates why game balance is important - if there's one really good option, it's hard to have a fun game that challenges the unbalanced character without making everyone else irrelevent or bored.
I can see why they did the weapon size rules, but they're too unwieldy IMO. I don't really like the entire move to make monsters more playable as PCs. I'd rather just have new PC races designed to evoke the feel of a monster, rather than duplicate its stats.
OTOH, I like a number of the changes. I like the changes to the paladin's mount (it actually makes it useful), and the DR rules are interesting.
Pet Peeve: I still think Moradin should have War as one of his domains. I have to chuckle with every warhammer toting dwarf that comes out in the D&D minis game. Those dudes aren't proficient unless they wasted a feat on Martial Weapon Proficiency.