Anakin's story wasn't engaging. The further it went on you never feel like this guy can be Vader. It comes out a lot in the Clone Wars TV show as well (which I like, all things considered), he's just too.. good. That and Padme was just bad. It wasn't just Portman, the whole Anakin / Padme story just never clicked. Like it was being forced upon us, but the two just weren't right. This goes back to my point about Anakin's story just being not right.
I do like some aspects of the prequels, and hate others. I can say the same thing about the original 3 though as well, though (Being that the first half of Return of the Jedi is just as bad as the prequel trilogy and no one talks about that). I found myself sticking to Obi-Wan (who had always been my favourite, even when I was a kid and all he was was the old Alec Guinness mentor), and the lightsaber duels were fantastic, and the new additions to the musical score never felt out of place. Space battles on the other hand, for all their CGI, never felt quite as thought out as the ones in the originals. Did lead to some fun games though, Battlefront 2 is one I've played a lot more than others.
EDIT: I disagree with the Jar Jar hate though. He really only partly ruined Phantom Menace, the kid playing Anakin did more damage I think. He wasn't even a factor in the other two, and actually had a couple interesting moments in the Clone Wars TV show. Bringing that up for the second time, I've got to say what I've said about the SW universe as a whole. The further anything SW is from Lucas, the better it is for it. The worst episodes are a direct result of his meddling.