George Lucas' life is a better meta-version of the prequels. Take that story and film it: everyone loves this dude, we think he can do anything, we throw praise and ambition onto him, and he inspires so many, and then he gets burned out on it all and gets too big of an ego, his personal problems begin to push people away, his marriage disintegrates around the thing he loves, and he hides himself away in his personal empire, and then lashes out at critics for not understanding the secret greatness of what he does. Lucas was Luke. Lucas became Vader...benignly, because making poor latter day films and being kind of nerd rage in response to criticism is not the same as planetary genocide and evil. Nonetheless...
So Anakin is this simple farm boy that's a great pilot. Kenobi finds him and basically makes him his squire, and the two grow into friends. The Clone Wars come, and they are basically this galactic crusade, where armies go off with total optimism to be gone for years at a time. Anakin goes off on this greatest adventure with Kenobi, with whom he's gone on many other such idealistic missions before. However, this one changes him. The Crusade turns out to be a botch where the Republic, corrupt as it is, engages in wickedness itself. To fight the enemy and their darkness, Anakin gives in to darkness -- fire with fire. He and his wife grow apart as he is gone for years, he falls into temptation, and gradually takes on the same evil he had fought until he stands before a Palpatine who points this out to him and he falls to darkness. "The galaxy needs order or it falls to chaos. The Clone Wars proved this. The Republic is old and corrupt. The only thing that matters is force and fear. We shall be the one's to secure it", and additional epic dialogue.
I would go back to square one on everything, and throw out everything that is not from the original films. For example, the Clone Wars was strongly hinted at as being the Republic versus an army of clone warriors. Keeping in line with Japanese films, my take would have been to have Palpatine pulling the strings of this clone army, and to have a group of basically Sith henchman underneath him, each like the boss level in a video game. They could be generals. And have Anakin defeat each of these unique Sith with whatever unique style they fight in, with the ultimate goal being that Palpatine was training Anakin and seeing if he was worthy, and then making him his lone apprentice.