When I originally read the book, I thought the title referred to Minas Tirith and Minas Morgul. They're the towers of good and evil, they're where the respective parties end up, and you get set up for the epic battle in the next book. But prior to seeing the movie I saw an interview with Peter Jackson, and he said that the title refers to Isengard (he meant Orthanc) and Barad-dur. I thought, "That's interesting, that's a different take on the story." When I saw the movie yesterday, I realized why he said it: Minas Morgul is gone!
I really understand you have to take things out to make the movie fit: you can't just translate the book word-for-word into a picture. So I didn't mind in FoTR that Thom Bombadil or the barrow-wights were gone (although I thought the movie suffered from having left out Gimli's interaction with Galadriel at Lothlorien -- I thought it was an important piece of character development). But in this case, the missing parts I think were really detrimental to the story. It also really bothered me that he threw new elements into the story: I thought they made the movie less interesting, not more.
The emphasis on Rohan rather than Gondor leaves you wondering why Aragorn cares about the battle of Helm's Deep. There's no real explanation of how it's connected to the quest to destroy the ring. That's why Peter Jackson had to throw Aragorn off the cliff: he needed to make the battle more dramatic, and Aragorn more connected to it.
And don't get me started on the elvish army marching to Rohan. If Elrond had an army, what the heck were they doing up to now? This was Deus ex machina of the worst kind.
I also missed Faramir's character from the book. There he's an interesting and thoughtful man, but here he's just another power-hungry human.
On the positive, I liked the oliphaunts and thought Gollum was superb. And Eowyn is as much of a hottie as I thought she was.