Personally I don't think the basic layout of the prequels was horrible, only that the execution was horrendous.
If left entirely up to me, though, I would have made the rise of the Empire and the making of Anakin into a Sith would have been more analogous to the rise of the actual Nazis. Anakin and Obi-Wan would be master-padawan but more like partners almost equal in strength in the run-up to the clone wars. Obi-Wan would be be a kind of brash and prone to trying to find easy fixes to problems, where Anakin is a model Jedi, being generous and always going out of the way to help others. At the beginning of the first movie they go on an important mission for the council to investigate some new buildup of forces, which ends up being a Cloning facility. In the process, they meet a female Republic spy who we'll call Luya, who while initially reluctant helps them escape, her and Anakin have chemistry based on opposites attract trope. They get back to the Council, and they lead an assault to destroy the Cloning facility, only to find out that the Big Bad has these facilities in more than one place.
The second movie would, once again, be all about the Clone Wars. The Republic is heavily engaged against the Big Bad, but the Jedi and only offering tepid support. Luya would be sent to sabotage some kind of war facility and got caught. The Republic wants her bad because she has important information. Anakin is a rising star in the Jedi Order, even earning a top military spot in the order, while Obi-Wan continues to be his partner and tries to advise him, but Anakin is finding himself more compatible with Palpatine, a member of the Jedi council and his immediate superior. Upon hearing about Luya, the two team up once again to save her, and Anakin takes his first step down into the dark side by killing innocents on the way to get her, only to find out that Luya freed herself. They continue their romance, largely in secret, Obi-Wan turning a blind eye to it, thinking Anakin a stronger Jedi than even him. When they get back, the Republic isn't doing so well against the Big Bad, and Palpatine maneuvers to take more direct military control, and employs more Jedi to the fight. Palpatine then asks Anakin to take control of the biggest battle, Anakin doing whatever it took to win it, including disregarding the lives of Republic soldiers. This causes a split between him and Luya, who is all-Republic. The final battle, which Anakin takes part in, injures him badly, forcing him to have a number of machine implants, vowing forever revenge on the current Big Bad for taking away his ability to have children. The final twist being that Luya finds out she's pregnant after splitting up with Anakin, not telling him.
The third movie would concern cleaning up the remaining pockets of resistance from the Big Bad. Palpatine and Anakin become a ruling duo of sorts, becoming more and more influential in the Republic over even the larger Jedi council. Palpatine urges the Republic to expand, taking over more and more planets, using increasingly ruthless tactics. Luya opposes all of this, and starts to organize an opposition resistance of Republic officers and spies like herself. She becomes the de facto first leader of the Resistance, pushing back against the fledgling Empire. The resistance splits the Senate and the Republic, with Jedi starting to join the resistance and the Council becoming less influential than ever. Luya has the twins but hides them fearing they will be killed by the Empire, intentionally or unintentionally. A huge battle is staged on a planet, Republic vs. Empire, Jedi vs. Jedi, and Anakin once again participates, eventually finding Luya on the battlefield. Luya tries to urge him to stop, knowing she can't win in a fight against him, while Anakin tries to get her to join him again. Obi-Wan, who has joined the Resistance, then meets Anakin on the Battlefield where they have an all-out fight, before Anakin is injured again by Luya, who shoots him before Anakin can kill Obi-Wan. Anakin then cuts Luya down in rage, retreating from the planet and ordering the fleet to bombard the planet to destroy the Resistance, killing most of the Jedi soldiers on his side as well. Obi-wan chases after Anakin after he retreats, but ends up having to run himself as the Resistance fleet is destroyed. Palpatine has already quietly assassinated the rest of Council still on the fence, and most of the Resistance is destroyed, save for a few scattered Jedi. The Empire takes full control and eliminates any trace of the previous Republic, continuing its war of expansion.