The prequels have two problems. The first is that they have deadpan pacing that never speeds up or slows down. It's like looking at a black and white photograph of a rainbow because the pacing doesn't evoke feelings.
The second is that after Boba Fett in the original trilogy, Lucas became outright paranoid of people liking villains. You IDIOT. Villains are more important than your heros because they have to evoke both feelings of attachment and disgust.
The way to fix the story goes back to Darth Maul.
1) Introduce a third sith in Phantom Menace--Maul's Girlfriend. Maul has been bleeding in the direction of a gray jedi because he's in a stable relationship, but Sidious isn't comfortable with three sith. So he sends both to Tatooine knowing one will die. Girlfriend and Qui-Gon trade lethal blows, and Maul suddenly becomes a true Sith. Sidious becomes a despicable villain and his henchman becomes a tragic pawn. Bonus points for using the pod race as eye candy while you establish Maul and Girlfriend's relationship.
2) Mitochlorians are dumb. You don't need a scientific way of proving Anakin is the Chosen One. You just need Qui Gon to believe it. Props for ripping off Mitochondria from Parasite Eve--totally wasn't expecting that--but Star Wars is a fantasy setting, not a science fiction one. Hard SF explanations will fail in high fantasy settings 100% of the time.
3) No more Count Dooku. Or General Grievous, for that matter. Maul is the only villain you need for most of the trilogy, and he can control his anger enough to do the same things.
4) I'll go out on a limb, Jar Jar is not actually a bad comic relief character. It's just the bland, heartless pacing the prequels have ruins his delivery on already iffy jokes and the gungan species design is...disgusting. Personally, I would just rewrite him as a luck tank and forget trying to be funny.
