I've been re-watching the prequels since I started this thread, and I think that there is one over-riding factor keeping the films from being pretty good. That's the silliness. The kiddie-fied universe.
The films are actually pretty decent-to-real good Star Wars films when the silliness isn't on screen. Darth Maul's two fights with Qui-Gon. No silliness and some of the best parts of Episode I. Contrast that with the Gungan battle--super silly and not so good.
The pod race should have been a big Star Wars wow moment. Instead, the stupid twin-headed race annoucer and all the silly drivers make it less memorable. Just think if the pod race had been with the realty used in the speeder bike scenes on Endor in Episode VI. Done that way, the pod-race would be awesome, I bet.
Again, Obi-wan's fights with Boba Fett, both on Kamino and in the asteroid belt around Geonosis. Cool Star Wars moments. But, the attack on the Trade Federation blockade, in Epsiode I, is silly the way it focused on a young boy "Now, this is pod racing!" coupled with the silly droids.
The standard dog soldier droids, with their "Roger, Roger," are down right silly. The droidekas (the ones that roll the pop up like spiders with shields on) are pretty cool and hold our attention more--because they're taken more seriously.
I've read that one rule Lucas had when filming the first film, Episode IV, was that people (studio executives and actors) kept trying to play the parts tongue-in-cheek. Lucas insisted that the material be taken seriously. That's why there isn't a lot of silliness in A New Hope (or even Empire). But, time progressed, we see more and more of it popping up in the films, starting with the silly band at Jabba's Palace and the Ewoks in Episode VI.
The next time you sit down to watch any of the prequels, ask yourself, "Would this scene be a lot more interesting if it were taken more serious and done without the silly parts?"
If so, I bet we'd all be jumping around with thumbs up for the prequel movies.
Even Jar Jar Binks. If he were more realistic and not as cartoony and silly in the way he speaks and acts, I bet he'd be a beloved new character added to the Star Wars line of heroes--at least on a level with C-3PO and R2-D2.
Look at C-3PO in Attack of the Clones, running around all animated on that silly conveyor belt on Geonosis. Not funny. But, look at how he was portrayed in Empire, or even in the new film, when he popped up between Leia and Han just as they were reuniting. THAT was humorous. And, it wasn't silly. C-3PO running around with his head attached to a dog soldier droid in Episode II, was silly and not funny.
My point: Remove the silliness from the prequels, and you've got some good films on your hands.
The silliness in the films just kills them.