The rash of fanedits we've seen of these particular films shows that all The Phantom Menace, Attack of the Clones and Revenge of the Sith really needs is just one more run through the editor's desk, by someone (ANYONE) who isn't George Lucas. Someone faithful to the intent of the scripts, but with a better eye/ear to what works and what doesn't. And who isn't OCD about getting the movie as short and fast-paced as humanly possible.
Most of what feeds the dislike of the prequels, it seems to me, is frustration. Because Lucas was so close to getting it right. Anyone who's read the screenplays or novelizations, or seen the deleted scenes that have been released, senses there are better movies hiding somewhere in all that CGI. All the right ingredients are there - they're just not blending together as they should.
I could see, say, extended 'Assembly Cuts' of the prequels that finished and put back in every deleted scene (except where Lucas chose to change the story, which would be in its own separate section of the Blu-Ray). Fox did that with Alien3 and Alien Resurrection in their Quadrilogy set, publicly noting that it was not done with the director's input, and both turned out better for it (the former more than the latter).