I feel like there are two groups you fall into if you defend the prequels. There are those who were young and grew up with the new movies, and those of us who had delved into the EU and knew that Star Wars could be defined in so many ways. I still like the prequels, but they are heavily flawed movies. Episode III was better because George, I think, realized that he had to go darker in tone, even though he still couldn't get out of that mindset of "where are the toy sales". And, as has been explored numerous times, the directing is still horrible. George believes, for some reason, that effects outrank story, and for that matter, acting. You have some really great actors in that film who just come off as terrible because of his direction, and because of that, you can't react to green screen sets and mo-cap creatures in a realistic way.
That being said, there are still two moments that make that movie rank pretty high for me: The duel on Mustafar, and Vader's mask being lowered down, creating the monster we all know and love. When we hear that mask seal and that classic respirator start breathing, I still get goosebumps.
