I think a fair criticism of the prequels is that they take themselves far too seriously. Sure. there's some light hearted moments here and there, but because the plot is centred around Anakin as a jedi and his transformation to the dark side, it has to go pretty dark. And to be honest, the dark stuff is handled very well. In Clones, the death of Anakin's mother and his reaction to it is a pretty intense moment that does a great job of foreshadowing what he'll become. His eventual transformation in Sith is also done very well, as well as the confrontation on Mustafar. It's the light hearted moments in the films that tend to fall flat, like the romance.
I think an underrated part of the prequels is the Trade Federation/CIS. While the political talk in Menace is a little overboard, they do make for a good adversary. The droid designs, especially the Droideka are all pretty cool, and unlike the Stormtroopers (the most they did was kill Owen and Beru in ANH), they're actually a legitimate threat that do kill a few characters, even if they are minor.