Most of the changes in FotR didn't bother me - because they were in character and some of them actually enhanced the story!
- Merry and Pippin letting off the fireworks at Bilbo's party etc. and Sam dancing with Rosie.
-I agree with you that it was much better to leave out Tom Bombadil!
-the shortened journey to Bree didn't bother me too much , although it seemed a bit strange how Merry & Pippin just run accidentally into Frodo &Sam , and then join them on the journey ...
- Pippin saying "what about second breakfast?" that wasn't in the book, but it fitted so well!
- I didn't mind Arwen replacing Glorfindel and I thought it was well done to show more of her, because of her story in the appendices.
- The council of Elrond was changed and much shortened, but well done. (In the book nobody quarreled)
- I think the depiction of Boromir was actually better than in the book! For example the scene where he teaches the hobbits how to use a sword, or when he picks up the Ring on Caradhras. Not to forget the dramatic death scene. I think his words to Aragorn were very much in character.
- Moria was great. The troll-fighting scene was too long for my taste, but it didn't really bother me.
(The worst things for me in FotR was the wizards fight and Frodo being so weak.)
In TTT most of the changes were quite drastic and
did bother me! Especially the changed characters! But I won't go into that here.
- the Elves in Helm's Deep weren't logical if one knows the history, but they looked so noble and I love the "martial Lothlorien-theme"music when they march in... so it didn't bother me too much.
- I thought it was quite ok to show Arwen , as she must have been in Aragorn's thoughts, and after all she was "watching over him from afar" (Only Elrond wasn't in character!)
In RotK most of the changes do bother me
.
- But I loved the scene in the SEE DVD where Pippin & Faramir talk together.