Yeah, I guess I thought it was implied that when I said a few more drafts, that problem characters/concepts like Jar Jar Binks would be included in those drafts. Im talking about this stuff happening before a single frame was put to film.
Personally, the prequels I thought Id see were this:
Episode 1: Obi-Wan discovers a young, but talented Force user named Anakin Skywalker, a headstrong 15 year old that he takes under his wing and tries to teach him the ways of the Force (some world building space shenanigans would be the B and C plots, but the movie itself focuses on establishing the relationship between Obi-Wan and Anakin Skywalker.). The movie ends with Anakin making a name for himself doing something heroic with his raw power, and gaining the attention of Palpatine, a cunnin and opportunistic chancellor. You can still use concepts like Qui-Gon and Darth Maul, with Maul killing Qui-Gon, and Obi passing on revenge, while Anakin is furious. No Jar Jar Binks as is, but Gungans could still be used.
Episode 2: An older Anakin Skywalker has grown cocky and overconfident, given his star pupil status at the academy, and his continuing successes in whatever space conflict we use as the backdrop for this film. He eventually begins to butt heads with his Master, Obi-Wan Kenobi. Perhaps Anakins desire for revenge against the villainous Darth Maul creates cracks between the two men. He meets and falls in love with a beautiful woman named Padme, and by films end, he has betrayed the Jedi Order (the B and C plots would revolve around the ascension of Palpatine and his corrupting influence on Anakin), and has killed at least one major Jedi Council member (ie, Mace Windu). The rub here is that Obi-Wan and the other Jedi dont know who the traitor is, and it is sowing discord and distrust throughout the order. Anakin is also unaware that his wife is pregnant, and their relationship is destroyed when she learns the truth of his slide to the dark side.
Episode 3: Anakin continues his extermination of the Jedi under the noses of the Council, sabotaging any investigations while Palpatine makes his final plays to become Emperor. Obi-Wan eventually finds out, and Padme is forced to flee with baby Leia, while Luke is hidden away with Obi-Wans estranged brother, Owen Lars. Anakin is led to believe that his wife was killed during all the kerfluffle and he blames Obi-Wan for not looking out for her.
The rest of the film is Anakin wiping out the remaining Jedi, and Obi-Wans pursuit of him, eventually leading to a confrontation on a lava planet where they battle, with Anakin seemingly falling to his death in the lava after Obi-Wan disarms him. He assumes his friend is dead, and heads off to Tatooine to watch over infant Luke. He doesnt know that Anakin is Darth Vader (save that for EU material where Obi-Wan learns that Anakin survived their battle, and that the Emperors mysterious new henchman, Darth Vader, is actually Anakin Skywalker). The B and C plots would be establishing the Rebel Alliance, Leia and Padme being hidden away with Bail Organa (again, more EU material can focus on Leias relationship with her mother and Bail), and the film can still end with nostalgic shots of Ben on Tatooine watching the Lars raising baby Luke.
I mean, thats the kind of shit that I had floating in my head before the prequels came out (obviously without concepts like Darth Maul, Padme, etc etc).
A lot of that stuff actually is in the prequels, but as I said before, the execution was piss poor. Starting with a little kid Anakin was the biggest misstep for The Phantom Menace. I still argue he should have been a teenager, but still younger than Luke was in A New Hope (hence, having him be 14 or 15).
In either case, it doesnt matter what could have been. The Clone Wars cartoon is all I really need from the prequel era.