The heroic Legolas scenes, more than anything, got under my skin. But that is only a small bit, and easy to ignore when looking at the big picture.
What I loved very much was the time put into every detail of the societies. From Hobbiton to Lothlorien to Mordor, and everything in between, the setting was magnificent and the costumes were lovely.
Also, I don't think anyone was miscast in any way. All the actors played thier parts to the best of thier abilities. None were fake, or strained in thier lines. So despite the fact that some of the characters were different, they were all played well.
I also must mention the music. The music was always perfect, matching to the feeling of the scene.
~and thus my thoughts cease~
(For now at least
)