Neither. I would keep the Lucas Prequel Trilogy as is and weave a new tale in and out of it, just to make things interesting.
I would focus on another character entirely, probably female, who becomes associated with Anakin during one of his Clone Wars missions. Anakin at this time has placed himself in hibernation in order to survive otherwise lethal wounds, and so he must communicate telepathically with this female protagonist in order to survive. He mentally guides her through piloting the ship, but as she is part of a gang of scrap merchants illegally scavenging the Clone Wars battlefields, she must avoid the Republic, and so they part ways at the end of Episode 1. Neither she, nor the audience, has even seen Anakin's face or heard his spoken voice, letting their imagination fill in the details of this legendary character.
Episode 2 focuses on our protagonist's growing aggression and the first hints of Force sensitivity (attributed to a subconscious mental link to Anakin), and her insistence that she should join the Republic and fight with Anakin. She secretly joins a squadron under the command of another Jedi, but Order 66 comes down the line and she only barely manages to save her Jedi commander. She almost dies herself, blacking out and thinking that Anakin has been killed.
Episode 3 shows that our protagonist is now seemingly without any power in the Force, attempting to serve her Jedi commander. It is also concerned with the children of the Jedi, including the child of Anakin, and with our protagonist confronting Vader in a final aerial combat. The Clone Wars are over, but the final battle of the Clone Wars has begun...
