If I can’t get rid of Jar Jar, I’d reduce his screen time greatly at least.
Re-cast Jake Lloyd in the first film. Perhaps age him up a bit to make the Anakin/Padme subplot in the first movie less creepy. (Yeah, I know Padme’s supposed to be 14 in Ep 1. Not buying it.) Make his character a darker and more brooding youth, not entirely abnormal, just with the slight sense that something is a little…off. Haley Joel Osment or that kid from The Ring come to mind as possibilties for the role.
I was going to say re-cast Natalie Portman due to crappy acting but then…I don’t know. Hayden Christensen gets a lot of crap for his performance in the prequels, but I don’t think he’s a bad actor at all. I think his performance suffered from crappy writing and directing, because his motivation during his transformation into Vader is all over the place, and that comes from the script.
Annnyways. My whole point is, I think Portman did a crappy job throughout the trilogy, but I’m willing to give her the benefit of the doubt and chalk it up to bad writing.
Padme would not die of a broken heart. What a load of garbage that was. I think it would work better for her to get between the Obi-Wan/Anakin fight at the end, but get hurt far more badly, and die due to her injuries after having Luke and Leia.
I think Darth Maul was wasted as a character. I think he should have had a bigger part, been present throughout the trilogy and finally get defeated in Ep 3. I think it works better in general to have your enemies fewer, but more formidable, than to have new villains crop up in every film.
No midichlorians.
The secret of how Obi-Wan and Yoda’s bodies disappear after their deaths needed to be addressed more than the throwaway scene we got at the end of Ep 3.
I didn’t actually hate the prequels, exactly, but was very disappointed in them. George Lucas writes some god-awful dialogue, but he’s fantastic at painting a picture. The last 20 minutes or so of Revenge of the Sith is very well done, I think. The shot of Vader’s mask being lowered into place is just perfect, and seeing the Organas with Leia on Alderaan and Luke being handed over to a young Owen and Beru on Tatooine was quite moving.
On preview, I see I’ve been beat to a lot of my ideas, but I’m going to post this anyway. This is all just off the top of my head. It’s been awhile since I’ve watched any of the prequels. I know there’s more I’d change, but I’d have to think on it for a bit.