It's be a VERY long time since I've watched any of the prequels, but I don't remember finding anything wrong with the score while watching TPM. It was probably the best thing about the movie, actually. I do, however, remember while watching ATOC in the theater for the first time, thinking to myself, "what the $%@$% did they do to the music?" It is a really obvious hack job & sounds terrible. ROTS was not much better.

That being said, of course there's going to be cuts/edits to the score for the final film. And sometimes it's the right choice. I'm sure many of you have seen the ESB duel with original music restored on youtube, but just in case, here's a link:

http://www.youtube.com/watch?v=brVI-Hy5Y2o

I think it works MUCH better with most of the music cut like it was in the final film. It makes the duel more gripping and emotionally tense/powerful over all with just the right bits of music to really emphasize that feeling at just the right times. The version with the restored music (with all due respect to John Williams) just feels much less powerful as a whole.