Here’s a list of changes that I will personally try to include in my eventual prequel trilogy that I think could work in this project:

Obi-Wan doesn’t refer to Qui-Gon as ‘master’. In my mind they are both Jedi Knights and equals.
Dooku isn’t a sith, rather a fallen Jedi. He has a Blue or Green sword.
Darth isn’t used for anyone except Vader.
Vader’s name isn’t spoken and his transformation isn’t shown.
Anakin and Obi-Wan shouldn’t antagonize each other throughout EP II.
Yoda isn’t seen in the Prequel Trilogy until Episode III where he talks to Anakin.
The Trade Federation and the Separatists should be one in the same. Perhaps they are the 'Separatist Federation."
Neimoidians speak in an alien dialect/don’t speak in a grossly offensive accent.
Jar Jar/Gungans are removed entirely from EP I. Jar Jar’s purpose in the plot is to set up the Gungan battle at the end, which we have no emotional attachment to because is is thousands of mindless robots and thousands of unnamed Gungans. I say that everything Gungan related is canned.
Less advanced holograms/technology. I mean look at Luke’s room in EP II vs EP IV!
Palpatine doesn’t turn into monster mash on screen.

I can’t think of anything else at the moment. Can’t wait to get started!