You could take all the special effects out of LotR and I still think it's better-made.
I felt a much stronger connection to the characters..they seemed to have more depth and development. Acting was definitely better as well. The weakest acting in LotR was from the guy who played Samwise imo. Liv Tyler may have had a few weak moments. Everyone else was pretty close to perfection.
But in Star Wars, even some of the more important characters slipped up a little. Carrie Fisher a bit, and especially Mark Hamill.
^ Someone mentioned the score...I've always thought of Lord of the Rings and Star Wars having the best scores of any film. But still, LotR's score is more powerful and feels like it had more thought put into it.