I just thought of another thing that might have improved the Prequels: Marcia Lucas' Editing. If you look at how the Original 1977 Star Wars is structured - A big opening battle to grab your attention and let you know this is going to be very cool, followed by some much slower pacing while the droids wander around in the desert and Luke complains about his chores. A lot of this works because of how it was put together in the editing room.

We also know (from Rinzler's making of Star Wars?) that it was Marcia's idea to add dialog to the Greedo scene when the Jabba scene proved to be unfeasable, which is why re-including the Jabba scene in the SEs is so pointless - Han Solo has to explain that "Even I get boarded sometimes" twice in as many minutes.

I expect she also helped to make the original trilogy better by pointing out things that just didn't work, whereas if you watch any of the docs on the SEs and prequels you get Rick McCallum telling us how great everything is, and what a genius George Lucas is, which is probably what he told George when he asked, "are you sure we're not going to far with Jar Jar?" I bet Marcia would have had something more constructive to say.