I truly wish some of the cues in Episode I's final battle had survived. I really like the additional footage of the lightsaber duel and believe the quick cross cutting in Part 2 ramps up the momentum of that sequence since the focus isn't on any one battle for long.
I've always thought Episode III's opening could have used more music to help with the rhythm of the sequence once they board Grevious' ship and the dropped music does help. I love the cue when you see Grevious' ship after Obi-Wan and Anakin have been captured. I don't know how anyone can watch those moments with and without music and decide the music free versions are better.