I mostly agree with Scythe above, except that the one thing I DID like about episode 2 was the way Darth Sidious (you might even describe it as... an insidious way...) manipulated the republic against itself. It's made even better in the Episode III novelization (In general I don't care much for Star Wars books, but Matthew Stover takes what might have been an average story and injects it with way more depth than I'd have felt possible), with the description of how the Clone Wars were the ultimate Jedi trap.
Well, I would not mind it if he still did that, but he needs to remain in the shadows about it. Remember how ominous he was in the early movies? You had Darth Vader but you only ever heard about the Emperor when someone spoke about his rule. Later on you see him for a few seconds with Darth Vader bowing and you are like "ohhhh shit" and then finally we see him in the final movie, sitting dark and evil on his throne.
The one thing I hated most about the prequels was throwing Palpatine all over the damn place. You see him talking with the Trade Federation, you seem him with Padme whispering in her ear. We watch him take leadership of the senate, we watch him get supreme power from the senate, all the mystery was gone, and we all knew he was evil anyways. The whole time they try to make it seem like they are different people, and the whole time we all KNOW he is the bad guy. Each movie we watch how he gains his power without any mystery.
You know what would have been neat? Having some "no-name" senator in the background. We barely see him, maybe one cameo, and then suddenly in the third movie he invades the senate with his army and the whole thing is over, or maybe through his own mental manipulations he takes it over, but not so overtly we have to see it on screen and KNOW its him so quickly. Then we could have that mystery of the untouchable Emperor continue on for the whole series.
Then again, I also hated the fact the whole "Luke, I am your father" reveal lost all meaning when kids know that fact the minute Episode 4 starts if they watch the movies in order of chronology. I feel like such a nerd.