A goodly number of them, though I have yet to fully sift through them all, and give a definitive "yea" or "nay" to everything. On the cutting board, however...
Paladin Mount. Bleah.
Weapon Familiarity. Exotic weapons are exotic because they're more difficult to use, not because they're strange and foreign, despite what the name says. It also inspires a good deal more homogenity; why should the dwarven fighter bother with any one handed martial weapons when the Greataxe is their superior, through and through? Dwarves are jiggy enough already.
Superfluous name changes. There was no necessity to rename Improved Invisibility into Greater Invisibility. I can understand trying to change the titles around just enough that they can be alphabetized by their related spells (Dispel Magic and Dispel Magic, Greater, and so on), but outside of that, many of the name changes didn't seem necessary. Improved Invisibility would have served just as well being titled as Invisibility, Improved.
Lack of Profession from the Fighter and Barbarian. It was essentially a flavor skill, as I saw it, and really didn't need eliminating. The one Profession that immediately popped into mind as being appropriate for both classes was Profession (Sailor). Seems a good, solid, appropriate profession for both. Particularly in light of the fact that both classes best represent what a Viking would have for their class, and should have access to Profession for their sailing needs. Seemed an unnecessary skill elimination.
The new damage reduction. Golf bags aren't appropriate for your average hero to tote around, and I prefer Nodwick's appropriate title to be henchman, not caddy. I also prefer that, hey, why sometimes, no matter how hard you hit something, you're not going to scratch it unless you have the appropriate material on hand - more in reference to the new aspect of damage reduction to be lowered, to allow for those power-attacking, greatsword wielding brutes to say screw damage reduction, and still dole out respectable amounts of damage, as opposed to the material types necessary. Over all...eh. Don't believe I'll make use of it.
Spell Focus, and company. Archmages and Heirophants, oh my. Ok, so perhaps the Prestige Classes, and Greater Spell Focus, both gave spells DC's that were a touch overwhelming, but Spell Focus, by itself, seemed a good, solid feat. I'm of the opinion it should have been left alone.
Buff spells. Altering a spell so people use certain types of magic items is unacceptable in my book. I prefer characters to be powerful due to who they are, not what they own. Now, the argument that the buff spells meant everyone was using certain tactics at all times, well, all right, I can understand that, but the mention that the change was to see more use made of magic items is not a good reason to make that change.
Oh, let's not forget, weapon sizing.
What else...hmm. There's a number of minor specificities, little details, like half-elves gaining Diplomacy, Rakshasa's changes, things like that, but I could go on forever with those complaints. Anyway, there's a good chunk of the changes I don't think will be seeing the light of day at my gaming table.