First, make Anakin's story much more tragic from the outset, without the slave deal but a Jedi accidently (maybe?) killing his mother when he is a baby. No Trade Federation, no useless droids, no Jar Jar, no force giving bacteria, none of that. The Jedi (possibly Obi-wan's master) takes the baby in grief and senses (NO KIND OF MEDICLORIAN DECTORS) that this child is powerful. He brings it before the council (not mentioning where or how he got it) and it is choosen to be trained. Anakin (played by a GOOD actor) is forced to be a Jedi under the tutorship of Obi-wan, for a "greater good." This all go fine and good, creating one of the most powerful Jedi for his age, always kept in the dark to keep his emotions, and thus powers, in check, until Padma (played, again, by a better actor) walks in when he becomes a teenager. At first it is just a simple crush, unrequited love. Since the whole, "Jedi can't love because it is a path to the dark side," and "Ambassador's can't fall in love because of duty." They silently fall in love, trying to hide it from both the Senate and the Jedi. The secret Sith Lord Palapatine (how he becomes the high cancouler doesn't matter) finds out about Anakin's secret love and dark past. He twists the galaxy around the political debate about Clones (had to include this bit since there was the mention of the "Clone Wars" back in a New Hope), until war breaks out between the revolting clones and the brain dead army of clones the Republic is using. During the confusion, Padma gets pregnet with Anakin's child and both the Jedi banish him, just short of him becoming a master. Palatine twists Anakin to his whim, telling how the Jedi lied to him about his family, how they killed him, how he wants to create a universe where "anybody can love anybody" by detroying the narrow minded Jedi. During a fight with his old master, Anakin gets beaten and barely left alive, before his Sith master makes him the black Vader we all know and love. Instead of ending it their, he goes to Padma, who rejects the metal monster he has become, and he actually kills her. When he leaves the body, the babies are saved at the last possible moment, they are split up, and we can go into the next films with no plot holes or story errors.