I think the prequel trilogy just wasn't pulled off right, period. Don't get me wrong, I still enjoy those movies. In fact, I jumped on the bandwagon when I saw Episode II and III and said that I almost enjoyed them as much as the original movies. It wasn't until I actually sat down and watched them all in order, on DVD in all their widescreen glory that I realized how much worse the prequels are. In fact, I've watched all 6 movies several times in order over the last year or so, and the more I watch them, the more I feel the originals are superior.
My biggest problem looking back on the prequels is that they just aren't believable. What the original movies had was realism and subtlety, everything from the real locations they were filmed at to the ingenious designs of the spacecraft. Even the love between Han and Leia was far more subtle and believable than Anakin and Padme's relationship, which seemed a little to forced and over the top. Sure, this is a sci-fi series, but it was a world (or, should I say galaxy) that we could easily relate to our own. Flight maneuvers in the space battles were patterned after real World War II dogfights. The imperials seemed like a real world empire, reminiscent of Rome or Germany. They were a much more believable (and menacing) enemy than the awful, bumbling, laughable trade federation with their cartoony (and just plain annoying) battle droids.
That brings me to my next point. Although the prequels have neat special effects, it seems so much more childish and cartoon like. I am aware that children are one of Star War's chief audiences, but it was as if I, II and III tried to appeal to much to kids and not enough to older audiences. In the original movies, sure, there were things that were obviously meant for a younger audience, but it also had a very serious atmosphere throughout the film. If you think about it, most of the creatures and robots in the prequels are a joke and can hardly be taken seriously at all. I think it's okay to have a few goofy characters in even serious movies, but I, II and III are chock full of them whereas the original movies only had a handful, and their goofiness was subtle .
My final complaint revolves around the plot holes the prequels generated. In my opinion, there are too many inconsistencies with the references made in the original movies compared to what actually happens in the prequels.
Anyway, that's my two cents. And, like I said, I still enjoy the prequels and even go as far as to say they're great movies. They're just not great Star Wars movies.