A few points:
Gollum's split personality argument was taken almost word for word from the book.
The books certainly do not feature ent/troll battles.
Faramir is no longer the same person at all. Although he did understand in the end, and come to his senses. And seeing Osgiliath was kinda fun, in a way. Same with Theoden -- completely done wrong for the rest of the story to make sense, IMO. Why does he have to want to run and hide and be all angry at Gondor?
Most of the characters go through very little evolution. Eowyn and Gollum are the only new characters we get to understand at all, Gandalf, Merry and Pippin barely seem to make cameos.
And I also was very underwhelmed by the ents attack on Isengard. In the book, that scene (narrated by Pippin to Aragorn, Legolas and Gimli) still gives me goosebumps every time I read it. I can just imagine the hobbits huddled in abject terror at the wrath of the ents, and the noise it caused. Here, the ents are vaguely ticked off.
Other than a few points, though, especially the lack of much character development, I absolutely loved the movie. Right now, I'd say I like it better than Fellowship, but I've only seen this once and Fellowship a number of times. We'll have to see how time lets this play out.