The Prequels needed some consistent villain (apart from Palpatine) that was present throughout (or at least in the first 2 movies), and played an active role in driving the plot.
I don’t think Maul really worked. He’s basically just like a “Generic Sith starter kit”. Yeah I know later cartoons gave him more depth, but he’s not ideal.
The Prequels needed a villain that fit thematically with the larger events/themes. Count Dooku is closer thematically to what I want, but he also sucks and is written incoherently. I like the idea that initially he seems to be taking a principled stance against a corrupt Republic, and he even outright tells Kenobi: “Look, there’s a secret Sith controlling everything, please help.” But then it turns out he’s actually just a Sith himself, so whatever.
After mulling it over in my head over the years, I’ve come to the conclusion that a character similar to something like Darth Revan would have worked best as a primary Prequel villain. The idea is that there was a formerly well-respected Jedi Master (like Dooku and/or Revan - I’ll refer to him as “Jedi X”) who was ex-communicated from the Jedi order due to a controversial but principled stance he took during a former war (e.g. how Revan went to fight the Mandalorians against the will of the Jedi.) The disgraced Jedi X goes into exile, where he by chance discovers that a powerful Sith Lord (Palpatine) is manipulating the Republic at the highest levels of government. Jedi X attempts to confront this Sith Lord and fails, and realizes the Jedi have no chance against this guy because they have no understanding of the Dark Side and nobody has even seen a Sith for thousands of years. So, with good intentions, Jedi X decides he has no choice but to become the Sith Lord’s apprentice, so that he can learn the Dark Side and eventually use it to kill his own master and save the Republic. (All this can just be backstory, it doesn’t need to be actually depicted in any hypothetical Prequel rewrite.)
But of course, the cost of becoming a Dark Side expert is that you actually become pretty evil. So Jedi X becomes a true villain, and his original intention of killing his master in order to save the Republic slowly morphs into killing his master simply to gain power for himself. But Palpatine is pretty powerful, and Jedi X (now officially a Sith) eventually concludes he can’t kill his master without help. So he starts looking for an apprentice of his own to help him take down Palpatine. During the course of the events of the Prequels, he meets Obi-Wan and Anakin. Jedi X opens up to Obi-Wan (in the same way Dooku does), essentially spilling the entire plot: “Look, there’s an evil Sith Lord secretly manipulating the Government. He’s way ahead of you and way more powerful, but I know how to take him out. Join me, etc.” Of course, since Jedi X himself has already done some pretty evil stuff, Kenobi doesn’t believe him.
Some time later, Jedi X makes the same pitch to Anakin. Anakin also doesn’t buy it. But Jedi X is able to manipulate Anakin enough, significantly pissing him off, so that Anakin eventually flips out and starts giving into his anger. Jedi X is hoping he can turn Anakin to the Dark Side by forcing him to act out of anger (in the same way that Palpatine tried to goad Luke into killing Vader.)
But… (plot twist), the plan backfires. Jedi X successfully goads Anakin into embracing anger and using the Dark Side, except Anakin is just slightly too powerful/unpredictable for Jedi X to fully control. Anakin gives into anger and murders Jedi X in a moment of rage. When Palpatine finds out, Palpatine realizes Anakin would make an even better apprentice than Jedi X. So Palpatine takes over where Jedi X left off in the effort to fully convert Anakin to a Sith.
Then, at the end of Episode 3, after everything goes to hell, Kenobi realizes Jedi X was right all along. Kenobi has a sort of “Statue of Liberty in Planet of the Apes” moment where he breaks down, realizing what idiots the Jedi (including himself) had been. He sees now that Jedi X tried to warn them, but they were too judgmental to listen, and now it’s too late because the President of the Galaxy is an evil sorcerer and Anakin turned into a fascist cyborg.