1) The loss of Concentration as a skill. Now there is a chance that wizards will botch that concentration check, rather than yawn before they roll a 1 and STILL SUCCEED.
2) The changes to Tumble. Some say it kills tumble, I say it makes tumble more than the "Oh for several levels I haven't put ranks into the skill because I always make DC 15 now."
3) Ranged Touch Attacks now provoke, like all other ranged attacks. Never made sense that magic had something special to it.
4) The changes to the skill feats and skill focus. The fact that putting ranks in the associated skills increased the bonus was nice, and a good way to encourage their use.
5) The loss of Synergies. I'd rather spend my skill points on skills I want, rather than on the skills I need to make my normal skill broken.
6) The new martial feats that took wizards from OMGWTFHAX to a manageable threat.
7) The loss of heavy armor from Clerics. Clerics are warrior priests but they were never knights, which paladins were. There was no reason for them to keep it with the advent of Paladins.
8) The changes to the Combat Maneuvers. Its really straightforward, and allows you to have a good gauge of what works, and what doesn't.
9) The toning down of notoriously bad spells. I'm looking at you Gate/Shape Change/Contact Other Plane!
10) The increase in bard power. Its subtle, but present. Most wont realize it till the bard has been long at work.
11) The inclusion of many things that help the GM's to learn how to build encounters, rather than the trial by misfire that I found the DMG to be for 3.5.
12) The loss of EXP costs for creating magic items, this often forced wizards to either invest, at the expense of being less effective at latter parts of a campaign, or to not invest at all for fear of falling too far behind.
13) The Nerf to the Spiked Chain. I'm sorry but there was a knight that kicked my butt with it, and I'm not interested in having a repeat performance. The reach was a bit much, and the loss of reach helped bring it back in line with some other abilities.
That's a good starter to the amazing changes I liked.