I feel that in Episode 3 alone could have done better with the rise of the Empire. I mean, the opening scene is an attack on Coruscant, the heart of the Republic! That alone should have caused some reaction. They could have used that to show the people's mistrust in the Jedi, thus leading to the Order's downfall and the Empire's rise.

What I plan to do for my rewrite's is to have the Republic's descent into the Empire similar to their historical Roman counterparts. During the last decade or so, Julius Caesar was assassinated by his fellow Senators and his great-nephew took his place, eventually creating the Empire following the deaths of Julius' assassins.

In my version, the Republic has finally recovered from the effects of the First Clone War against the Separatists (who were formed much earlier than in the actual prequels). Chancellor Valorum is coming to to disbanding the use of cloned soldiers, but the Clone Masters/Kaminoans (who provided the clones in the first war) and some senator don't want that to happen. Thus, they and the Sith to assassinate Valorum. It works, but the conspirators are declared enemies by the newly elected Chancellor Palpatine and thus side with the Separatists, leading to the Second Clone War.

Palpatine, being a Sith, pulls strings in the Republic while his apprentice, Maul, manipulates the ranks of the Separatists. The war would carry on, degrading the Jedi and the Republic, the latter of which turns into the Empire (maybe by Episode 2). The war would carry on until the Jedi Order's finally wiped out.

That's my idea. I plan on making some tweaks and hopefully, it'll turn out for the best.