Good:

5. Warrior specializations. This turned a very poor class into a very good one.
4. Assassins being made completely spell-less. Another awesome change. Take away some of the obvious no-thought power and give them a whole whack of skills.
3. Removal of necro acid blast and general improvement on the whole class.
2. Conjurers. A great class with a whole lot of fun stuff in it.
1. The entire economic revamp. A fantastic change which actually put worth into money.

Bad:

5. Empowerment. This is bad for a couple reasons, but the most glaringly obvious seems to be the pigeonholing of priests into bad religions. Some good religions, but a lot of horrid ones.
4. Removal of the Shadows and Knights. The one good-aligned cabal around I enjoyed. Fortress is no comparison, and when you threw every single good-aligned guy into the same building it was far too tough to raid.
3. Legacies. "Oh, let's just make the easiest class in the game to play even more powerful by giving them legacies. Shouldn't #### up the balance too hard."
2. No mage cabal other than Scion, and even then when Scion was crying out for a little relief from the pressure you added Outlander into the gank mix.
1. Sylvan. Awful, awful, awful. The age of "stupid gank squad".