I’m not sure if this could be accomplished, but I had an idea that Padme and the Jedi would actually be at opposite ends of the political spectrum throughout the prequels, (probably with Amidala supporting palpatine), and that a big twist mid-episode III would be that mace windu was working with dooku to assasinate Padmé throughout the movies.
This would give Anakin much better motivation for switching sides IMO, and be a surprising twist that the prequels sorely lacked.