They changed the races and classes quite a bit. Each core class (non-prestige) has a big thing that they get at 20th level to encourage staying in one class. They also get something special every level so you never have a level that you just get a change in saving throw and base attack.
They took the level adjustment away from noncore races. They changed favored classes, so now they're no longer based on race. You pick one favored class at first level and get 1 hp or 1 skill point (or something special for a few) every level you take of the class. Every time you level, you pick which favored class thing you get. Every race now gets a stat bonus of some sort, too. Humans and half humans get a +2 to a stat of their choice, while the other races have +2 to two set stats and -2 to a stat.
There are also a lot of little tweaks like not needing to make a touch attack for things like trip. Trip is now one of many combat maneuvers, which are standard actions to do.
Oh, and how could I forget? Almost everything is now crittable and sneak attackable. I think just oozes and elementals are immune.
They also condensed a lot of skills. Spot, search, and listen are all now one skill - perception. A lot of other skills had that happen, too. It makes it a lot easier to get the skills you want.
Oh, and they changed how often you get feats. You now get feats every odd level. It makes the characters very powerful (so they buffed up the encounters you do, too).
I really like how the classes have changed the most. They added neat little abilities to a lot of the classes that they get every few levels. Rogues, for example, get a rogue talent every other level (and +1d6 sneak attack the other levels). Rogue talents range from doing something nifty with sneak attack to getting an automatic roll to see a trap within 10 feet.
Well, I think I wrote enough. What a mess, hope it's understandable.