I new on this forum, but I've been watching it for quite a long time. Sorry for my mistakes, I'm not English native speaker - please, be lenient.
So first, I should point that in my opinion none of the fan editors could make the prequels good. They're beyond saving and they can only be made more watchable. The only salvation for the prequel idea would be if LFL/Disney would give a permission to make a prequel fan-films.
All right, enough with the introduction, back to the topic. So what about making prequels watchable? I really loved the idea of making the missing planet Geonosis, Qui-Gon Force ghost. Also redoing few characters and redubbing them could give more plot details to the audience and what the heck is going on in the movie.
The big problems with the prequels, especially in Attack of the Clones, are characters, plot and the villains. So my point would be to stick to the idea "make Anakin a bigger part of a larger story", Obi-Wan as the protagonist of the prequels, better plot and the villain for the whole trilogy.
To begin with, Anakin should be the same kind of character like Han Solo, we meet him in about half of the movie and he's like a secondary main character. He should be played as a good guy in Ep.I, good friend and a cunning warrior in Ep.II (maybe with some hints to his evil side - I'll get to that later) and in Ep.III he should be put in a situation, in which he has to choose between loyalty to his best friend Obi-Wan and securing the peace in the Republic/Empire.
Now, the plot. It should be made simple - no political boredom in the Senate. Let those scenes be played like in original Star Wars (conference room on Death Star, for example). Why the Federation couldn't be replaced with some opposite to the Republic but smaller galactic organisation that wants to conquer Alderaan (yes, Alderaan, not Naboo - if you're looking for explanation on that watch "What if Ep.I were good" by Belated Media). The "Federation" would be manipulated, but not brainless, like the original, by Lord Maul/Darth Vader (I'll also get to that later). Maul should be like Vader in Ep.IV - he seems to be the only evil force user, but surprise - he's got a master, that's more powerful than him! The story could play like in the original Ep.I - we get from Alderaan/Naboo to the Tatooine, next to the Coruscant and back to the first planet. On Coruscant Padme should visit senator Bail Organa (that would need changing the actor or finding the Jimmy Smits lookalike). Then Obi-Wan Kenobi would organise the whole "damn fool idealistic crusade" to retake Alderaan. There he would loose his friend Qui-Gon, because of Kenobi's recklessness. Also, there was a blokade surrounding the Alderaan/Naboo. Why Anakin couldn't prove himself as a pilot by passing by it (Star Wars: Obsession comic books).
The second film should open like the Bond movies do - with some kind of a fun adventure of Anakin and Obi-Wan, that somehow ties with the main plot, which wouldn't be like several different boxes of puzzles dumped on a floor. The clones would be the bad guys and the Republic Stormtroopers would be normal citizens pushed into the war. Dooku should be made a red-herring villain. The audience would think that he's the bad guy, but I see him as many others on this forum as a rogue Jedi, that sees the decay of the Republic, corruption and Sith control in the Senate. and here's the first part of ROTS in the AOTC - the movie ends with Dooku kidnapping the Chancellor and the two Jedi Knights are rushing to help him, then Anakin goes to far and kills Dooku. The movie might end with Anakin actually leaving Kenobi in the duel place with Dooku and Skywalker choosing to stay with Palpatine. OK, enough with those plot ideas, maybe one day I'll right it down.
Concerning Maul. He would be the first Obi-Wan's apprentice. But Obi-Wan was a little too eager to train him and unexperienced, so Maul turns to the dark side. Then he finds Palpatine and becomes his apprentice.
In the end of Ep.I Maul woudn't be cut in half, but he'll run or fall out of the window - whatever. In Ep.II he's like a shadow, that follows the protagonists, hires the Fett and makes the galactic war come true. Maul/Vader would be a human/near-human species. He's dark side turn would change his look (tattoos). Obi-Wan won't recognize him in Ep.I, and in Ep.II, there would be a reveal of him being the long lost Kenobi's apprentice (mirrors the situation in Ep.V). In Ep.III Obi-Wan would look for him, trying to capture or redeem him (Maul would take place of Grievous).
Now, the triangle Maul/Vader/Anakin. Have you seen the Lost TV Series? The relation between Anakin and Vader would be like Locke's father and Sawyer. Anakin would kill him in Ep.III and take his name. Obi-Wan would track down Maul/Vader to Mustafar, then he'll spill the beans about Palpatine being a Sith Lord, Anakin wounds Maul, next is the duel Obi vs Ani, Obi-Wan wins, and the finale of the Mustafar fight - Maul wants revenge and floods the area, where lies Anakin, with some kind of chemicals (it seems logical, more than lava. The chemicals would give him a lung cancer, hence heavy breathing). Obi-Wan rushes to Maul and pushes him into the toxic river, which he unleashed. Anakin and Maul are taken with those chemicals, and we have a scene like in '89 Batman - the hand comes from the pool and we keep the surprise in TESB. Maybe there could be a scene, where Tarkin finds badly burned body on Mustafar and puts it in the armor. Oh, and by the way, as the final battle in Ep.III I see the battle in the Jedi Temple and in the same time there's a duel between Samuel J. Windu and Palpy - later Vader arrived from the battle and kills Jules L. Jackson.
These are my ideas for the prequels radical edits. They're not quite thought out as a whole story, if I find time I'll rewrite and post it.
I hope you'll find some interesting ideas in my post.