This quote is kind of what gave me the idea,
"I thought... what if Star Wars was originally a noir movie from the '40's and '50's, very old-fashioned and in black & white? Later on in the seventies or eighties, they made the very popular Star Wars trilogy, but this is the original film made a long time ago. Imagine that it's another thing Lucas suppressed!"
Imagine it this way, this old noir film from the 40s or 50s was a tradegy. It had a young hero, Anakin Skywalker, he takes his job very seriously and neglects his wife, not intentionally, he loves her but he is just so caught up in his work. Also he has a ton of respect for his mentor, Palpatine. Palpatine starts to let him on on secrets, how somebody on the inside, somebody on the jedi council, or perhaps all the jedi council, have been manipulating this great intergalactic war that has lasted for years. The whole war is all their doing, perhaps because the law states that during times of war the jedi hold some sort of emergency powers, while at times of peace they are little more than security guards and police officers. Of course he is really being manipulated and the real ones behind the war are the Brotherhood of the Sith. A denomination of he jedi cult who are more free with their emotions where the jedi surpress their emotions. Maybe at this point the jedi doesn't even see the sith as evil, they are merely an unorthodoc version of the jedi. They haven't caused problems, they are force users but they haven't openly used their powers to cause problems. Perhaps a few jedi are weary of them, but as it is they are just a cult. Maybe they even go around doing good deads.
So anyway the story progresses and Anakin is slowly being convinced that the jedi are evil. Meanwhile his wife leaves him. Sometime later something comes up that convinces him that his closest friend Obi-Wan stole her away from him. this turns him more from the jedi. He joins the sith, and at this point they tell him more secrets, that there is a big plot to over through the jedi and end this war forever. The sith could start a war against the jedi, our story could end in a tragic showdown between two best friends, Anakin and Obi-wan. Obi-wan, to his own remorse defeats Anakin. The story, being a tradegy could end with the death of our hero, and then give an epilogue of how the Sith Lords after a long war with the jedi, destroyed them all and took rule over the galaxy.
Now many, many years later you want to make a sequel to this movie, but the first one was pretty closed ended. What do you do? Well the main character's wife left him, lets say she was pregnant at the time. There is our protagonist right there. We need an antagonist, he could be one of these sith lords, maybe not many of them are left, perhaps they all killed each other off. (remember, it is mentioned that Vader is the last of their kind). Also we need somebody to give guidance to our young protagonist, maybe Anakin's best friend lived and has been watching over him since his mother died and he had to go to live with her only living relatives. Everything from Star Wars (except for Obi-wan killing Anakin) fits perfectly, even though we have information gaps, we don't have near as many plot holes.
second sequel, it turns out another jedi lived the sith war against the jedi, and that Darth Vader is really Anakin and he didn't die after all.
Third sequel, we find out that Leia is Luke's sister and that Anakin's wife had twins. Obi-wan knew the Sith Lord Palpatine knew Anakin was very powerful in the force and that it would have been passed on genetically if he were to have children. Perhaps the sith are very misogynistic or something so Obi-wan takes the male to live with her relatives where just in case the Sith Lord looks up Padme in search of new apprintices.
And this is just off the top of my head, but it is amazing how many plot holes you can fill if the story is completly redone rather than trying to do minor re-edits to the existing prequels. I think having Padme live makes Return of the Jedi's "do you remember your mother", "she died when I was very young" and "I never knew my mother" work much better.
Sorry for my long post, I'm afraid I don't have time to make it shorter.