The ENTIRE POINT of all three movies is to explain why Anakin goes to the dark side, but aside from a few really poorly placed and obvious hints, it gets a total of maybe five minutes in III, none of which make any damn sense. Seriously, he goes from 95% nice guy with a small dark side to baby killer at the drop of a hat, because he is for some reason very easily convinced both that his wife will die and that magical darkside powers are the only thing that will stop it. Then he murders his wife almost immediately, because somehow he has absolutely no hesitation about pursuing the course of evil, while he did nothing but ponder and snivel the whole damn time he was light side.
Gah, I'm changing my vote for the worst film back to three. It had a chance of being good and redeeming to some tiny degree the other two movies and completely blew it.
I agree with you definitely on the point about Anakin. His transition to the dark side should have took longer and spread throughout the prequels more, and there should have been a better reason other than that he had a dream where his wife dies.
My biggest gripe was how easily the jedi fell. How does the most powerful force in the galaxy get wiped out in one day? It's still kind of funny how some of the jedi masters fell in seconds, yet you have one of the kid jedis, the one Senator Organa saw get killed, was able to not only to sneak passed Anakin to get outside, but killed a bunch of troopers before being shot. It didn't make sense!
As far as Episode I, which I hate the most, the most stupid things: jar jar (obvious), actor who played anakin (sooo annoying), how Anakin comes into the service of the Jedi (win a pod race, become a jedi), and how Anakin destroyed the space station at the end (he doesn't know how to pilot the ship, yet he beats the bad guys)
I could go on about how stupidly everything happens in all the prequels, but it would take too much time.