There were plenty of bones to pick with PJ's rendition. The radical departure from Faramir's true character. Frodo's portrayal as a simpering weenie. Gandalf smacking Denethor in the head. Aragorn's reluctance. Gandalf's humbling before the Witchking.
Denethor's flaming plunge of death. Frodo telling Sam to leave. Sam leaving. Legolas's brilliant wit ("A diversion"), Gimli's use for comic relief, Arwen's fate suddenly and inexplicably being "tied to the Ring"...etc.
Yet, despite all my intellectual quarrels with plot differences, the movies (especially Return of the King) stunned and amazed me. They blew me away when I saw them in theaters, and at home. I just recently completed watching the trilogy again (with a younger brother who was finally old enough to see the movies) and I have yet to see any movie that compares. The glory of so many moments -- the whole battle of Pelennor (especially Theoden's speech and the Ride of the Rohirrim) Sam and Frodo at Mt. Doom, Aragorn's "For Frodo" death charge, Gandalf telling Pippin about the Grey Havens, the very end of the film at the Havens (which chokes me up just thinking about) -- all of this redeems the film and more.