Mostly covered above...
I like how 3.5 psionics isn't broken out of the box and is actually playble with minimal house rules, without being pathetically weak or so overpowered it boggles the mind.
The skills, feats and ability score system convinced me to play 3e (as opposed to 2e's version, which drove me to playing Alternity, still a very fun system in it's own right).
The rules are, for the most part, consistent. Surprise rules actually work (I hated how 2e how two totally separate surprise systems - what about elven thieves?).
CR system. Wealth per level system (although the amount of assumed treasure is way too high, IMO).
You can actually craft cool magic items, since there are rules for that.
Level adjustment... yes I know it's not perfectly balanced, but at least now I can play a thri-kreen (with an understanding DM) who won't think I'm being a munchkin.
I hated 2e's saving throw system, (N)WPs, lack of balance, XP values all over the place, and turn undead (which, alas, didn't get changed for 3e). Oh yeah, and a profusion of frequently broken kits... oh wait, that didn't really go away, did it?