My PT would go like so:
E1}} Prettymuch have it be about the life of a jedi, introduce us to the order, how people are chosen, how they train, etc. In the end I'd keep from TPM, The Duel of the Fates ( which to this day I think is the greatest lightsaber fight on film. No CGI bull shit doubles or artsy glow stick dancing. ESB's the most dramatic, but for pure spectacle this is the king.) None of this crap about balance or midichlorians. Anakin's a teen from coruscant or naboo, whatever, and a reject from the council like we saw in TPM who quigon sees great potential in and believes his destiny is to defeat the sith, so he urges obiwan to train him. the end. Either that or Obi-wan discovers this young scruffy lookin hotshot pilot who's rejected and who has great great potential and Obi-wan offers to train him against the counsil's wishes. The plot would concern a coming war between factions within the republic and the protection of a senator rather than queen who Anakin falls in love with. It'd be a great story.
E2}}Clone Wars Parts 1 and 2. This replaces Attack of the clones, since it is more fun like the originals, has better quality acting, more badass jedi, Anaking being the best star pilot ever, and has a story with grievous actually being a threat instead of a dumb joke of a character. I'd have preferred these be made in live action instead of whatever lucas came up with.
E3}}And Lastly Parts of RotS... the good parts. I thought Ian's performance was brilliant. So all that should be kept except the silly faces. Get rid of Hayden and put in someone who can act. Oh and I'd never have had Anakin be younger than padme. What the hell was the point of that? They'd be around the same age. I'd have anakin build his red saber instead of that not so subtle brother vs brother thing Lucas decided to do and have Obi-wan take anakin's saber for apparently no good reason except that he has it in ANH. Just have Padme return to her apartment to find a lightsaber with a note attached saying "give this to my son when he's old enough." or something like that. the eyes turning yellow is great though. I like that.
Here's the mess. How does padme die in a non-crappy PT? well it won't be because George Lucas lost the will to keep her alive or some other dumb excuse.
My idea is she'd have the twins, then instruct yoda and KING organa to protect them, while she confronts the chancellor to discuss returning to democracy, not knowing he's a sith lord now. And the Emperor kills her before Vader's eyes. Oh and the reason anakin becomes a sith isn't just to protect his wife from some bad dream. His own lust for power and glory will be his undoing as he starts to like the taste of the dark side that he felt in the clone wars cartoon and embraces it fully once his old friend Palpatine offers him a chance to become great, and it's this chance to protect his family, have unlimited power to stop the endless war that drives him finally across the rift between the dark and the light.