A number of things toward the end of Return of the Sith irritated me on my first few viewings. One is the clownishness of certain moments in Palpatine's duel with Yoda -- the way he gets flipped backwards over his chair with his skirt up, the way he squeaks and squeals while dangling from the Senate hoverdisk.
Another is the "Frankenstein" moment when Darth Vader breaks loose from the medical table after his transformation -- not to mention the outrageous wimp-factor in his dialogue thereafter, and that ridiculous, "Nooooooooo" that he emits after being told Padme is dead. We waited 22 years to hear James Earl Jones speak as Vader again, and that is what we get?
But, as usual with the prequel films, when I asked myself if there might be method to Lucas' seeming ineptitude, a door opened wide for me. In this case, things clarified themselves after a conversation I had with a friend of mine. Bob complained that Lucas had done an interview recently in which he described Darth Vader as essentially a dupe and a schmuck in the original trilogy. This really aggravated Bob, who, like all of us, had always thought Vader to be the ultimate in cool villains. He felt cheated to hear Lucas badmouthing a figure who was of such primal importance to him.
And that, I think, is exactly the point of the way Vader and the Emperor are handled at the end of Episode III -- to tear down the notion that bad guys are in any way admirable. For almost 30 years, people have been seduced by the power and majesty of Darth Vader, and that seduction represents the fool that lives in all of us. Palpatine comes out on top in ROTS because the Jedi make a ton of big-time mistakes. Anakin turns to the dark side because the Jedi are not there for him in the way that he needs them to be. There is nothing praiseworthy, noble, or deserved about the triumph of evil at the end of the film: evil merely happens across one of those moments when good leaves the door unlocked.
Ultimately, the truth is this: villains are disgusting and pathetic. They win only when heroes fail, and when the public fails to recognize them for what they are.