This is probably well beyond the scope of any re-edit, but it bothers me that the main thing the Jedi have against the Emperor is that he's a Sith lord.
General Greivous dies, then the Jedi go full battle ready to arrest the man. Is being a Sith lord technicaly illegal? They have no proof or evidence that he's done anything wrong. The man doesn't even have a single session of the Senate to renounce his emergency powers. It just seemed really rushed.
Honestly, I don't mind TPM, although about 60% less Jar Jar would be nice.
AOTC is just unpleasent to watch. I hate Annakin the entire time, and they never actually solve the mystery Obi-Wan is investigating.