I think it would tie the trilogy together better aswell. For example, it was also remove the whole clone investigation on Kamino. I think how this would be done is to represent the Federation as the Separatists straight from the beginning so when Palpy says he will “eliminate the remaining threat of the Separatists” (or whatever) it will make more sense.

Another idea would be to make Jar Jar one of the Naboo representatives in TPM. This way we can see Palpatine purposely invade his planet in hopes he will give him power. This can be done by showing the Gungan battle at the beginning of the film, but edited so the Gungans lose the bout. This would give Jar Jar more of an arc and erase his antics from the film altogether.