The treatment of Faramir's character.
I'm so with you on that WR!
The Faramir of the movies was nothing like this most noble man in the book (with only Aragorn to equal him in his integrity).
I read that they changed Faramir's character as they felt his conduct might disenchant the ring. In the book he actually says he wouldn't pick up the ring if he found it lying beside the road. I kind of understand why they would change that in the movie after we saw the impact the ring had on the other character, but I still think that they made Faramir too "evil" in the film.
Denethur. The proud, noble stewart who called for Prince Imrahil's help and actually had a reason for being as insane as he was, or the nearly motiveless madman from the films. Hmm........
What I considered the worst thing was the way they depicted Denethor's death in the movie. I consider his suicide a really impressive scene in the book. You can kind of understand what drove him to madness. Of course they showed his immense grieve over the loss of Boromir in the movie, but they failed to mention his Palantir and the active efforts of Sauron to drive Denethor into despair and madness by showing him the huge armies that were to move against him.
For lack of a better word I must call his death in the book "stylish". Climbing onto the pyre, breaking his staff, clinging to the Palantir and lighting the pyre. Even inspite of the clear madness he had shown before there was something dignified about his depature.
In the movie they stripped him of that dignity which I found a really inappropriate thing to do. In the movie they didn't even let him ultimately choose his death, but rather let him be kicked into the fire by Shadowfax. The most tasteless thing however was to let the poor Steward of Gondor run all the way just to drop down the cliff for spectacularities sake. How could he even run that far (almost half a mile I reckon) while he was completely ablaze?
If I was to pick one scene from the triology where I would say Peter Jackson messed really up I would pick the scene of Denethor's death.
I mentioned the lord of the rings audio play which I have before. The death scene of Denethor is really impressive in that play. The voice actor did an excellent job in making his voice sound erratic in some, yet almost composed in other moments depending on what was said. There was a very fitting music in the background too. I suppose my vision of Denethor's death was strongly influenced by the audio play.
Gollum. Never in the films did I ever get the sense that Gollum was at all dangerous. In the books, he wa sboth dangerous and pathetic all in one. In the films, he's just like some lost kid with deformed features.
I admit that he appeared rather friendly. They might have done better if they had shown some scenes in which Gollum is tempted the way he is in some ROTK scenes when he sees the ring. Personally I was too impressed with the performance of Gollum in general to count this as a major lapse in the movie, but I see why you do.
Treebeard. A wise old entity of the forest not knowing that Sarumon was chopping down the trees? Eh? WTF!
They overdid the lack of determination on the part of the Ents. While in the book it does take them days to get roused, they do get roused without first deciding that they wouldn't join the war. I strongly suppose they did it to have that scene in which the Ents finally do get roused right in front of the gates of Isengard. They probably meant to keep the audience at suspense as (to those who don't know the book) it might have taken some of the excitement away if they had known all along (during the desperate fight at the Hornburg) that there was still a huge army of Ents and Huorns ready to smash Saruman's forces. Again I must confess I wasn't too bothered by this.
Another scene from the Two Towers which DID bother me was the supposed death of Aragorn and his return to the others. It wasn't in the book and I didn't feel it really contributed to the movie in any positive manner. I suppose they included it to have Arwen into the movie once again.
An earlier plan was to let her join Aragorn and the others in Helm's Deep along with the elves (who weren't present according to the book either). I suppose they had to include the elves to make the audience happy (and gosh, those elves ARE cool

), but I'm kind of relieved that they kept Arwen out of it at that point.