I'm not against the idea of Palpatine being behind everything. It's just that once again the film handled it in such a ham-fisted manner that they had to pull a "Our ability to use the force has been diminished" out of their arse in order to make their ****ty intrigue story work. And even so, it ends up with the Jedi council actually being surprised that the guy who kept voting himself more and more emergency powers was actually a bad guy when they should have seen it coming a ****ing mile away. Palpatine should have been someone the Jedi saw as a strong ally right up until the betrayal. The film did try to give that impression but it did it in such a bad way that it never rang true. Either that, or they should have given him a proper Grand Vizier role and had him secretly whispering in the ear of his puppet from a place the Jedi wouldn't see him.
On top of that, I wouldn't have minded the whole "Palapatine is in control of everything" plot line so much if we got to hear a little bit more about what the Trade Federation (in the first film) and the Separatists (in the second film) hoped to achieve. The big problem is that the films are such a mess that they are the bad guys cause they are the bad guys and that's all you need to know. You would think that when Dooku is revealed to be a Sith lord some of them might have thought to themselves "Hmmmmm, when did I agree to follow the Nazi party? Maybe that was a bad idea. Maybe I shouldn't do that." But no, they all merrily trot behind him and then act surprised when they get betrayed.
That's why Dooku turning out to be a Sith (worse still, a Sith controlled by Palpatine) was so disappointing to me. If instead he'd been an actual upstanding Jedi who Palatine had manipulated without revealing himself, it would have been a much more interesting plot line.
Finally, I have an issue with the whole Vader as the second coming plot line. He wasn't even in charge in A New Hope. It's only after the death of Tarkin that Vader becomes the second most powerful person in the universe. In A New Hope Vader is just the Emperor's go-to guy. That all got retconned somewhat in ESB but the prequels could easily have tried to explain it. It would have been nice if the films had shown Vader as someone obsessed with hunting down the Jedi to the exclusion of all else. That would make it very easy to slot him into ANH as someone who preferred to be in control of a single star destroyer chasing down Jedi and then later the Rebellion rather than someone who was in charge of everything.
