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.

And they have no record of the Sith doing any wrong for 1000 years or so :)