Surprisingly I've only just discovered this thread.
My wishlist for the prequels is as follows. Obviously some may be impossible or involve too much refilming/composting to be realistic:
1. Never have Yoda SEEN in the prequels. He can be mentioned as having been consulted as if he's some great unseen monk living in self imposed isolation (like some Tibetan monk seeking enlightenment) or even seen via hologram, but the hologram would be just a regular hooded obscured figure that looks nothing like him. So then Yoda would be concealing his true appearance to everyone and becomes a Wizard of Oz type character. I think that would work perfectly and uses a very well known character archetype that suits Yoda down to a tee.
2. Have another apprentice for Obi Wan. Perhaps we meet him in ROTS when Anakin is a fully fledged Jedi. It just needs to be hinted at that he's somehow gunning for Anakin. We can even use Hayden Christensen as the "bad" apprentice and......
3. Recast Anakin with someone who:
a. Looks more like Sebastian Shaw
b. Can act
4. Never SEE Anakin becoming evil, even though he is. We can still see Vader's misdeeds, but only in costume. It may seem very 'Fight Club' esque having it be like he's got Sith Schizophrenia, but it's a very good way of doing it to have a Darth Vader in the prequels whilst preserving the revelation of ESB as well as keeping Anakin as a person we at least think is good.
5. Have the Fight occur between Anakin and ObiWan's apprentice instead. So between 'New Anakin' and 'Hayden Anakin'. Now this is a big one and probably wouldn't even be possible and I'm not even that sure I want this as a change, but it would fix everything. Ben would still be technically lying by saying "Darth Vader Killed your father", but we wouldn't know that until ESB and then Ben's Ghost explains he was telling the truth "from a certain point of view" in ROTJ. In ANH, we'd be none-the-wiser and believe that this apprentice of Obi Wan became Darth Vader having "betrayed and murdered" Luke's father.
7. Have the Republic army (the precursors to Stormtroopers in white armour) not be clones. Instead replace the Droid armies with pale eyed, pallid skinned men in armour and call them "Clones"
I'm having trouble posting pictures for some reason so here's a crude mockup as a URL:
http://i5.photobucket.com/albums/y161/welsh_anarchy/603206_581635721852014_1667331729_n.jpg