The prequel movies are overall underrated, or over-criticized. But you have to break it down more to get to the root of why.

1) CGI - Lucas said he waited to make them until the CGI tech was ready to accomplish what he wanted to show. But he was almost the first to use closer to modern CGI, and it was a bit clunky but more importantly, it wasn't a language that audiences understood. Watching those movies, for audiences used to practical effects, was like walking into a room full of people speaking another language. Now, looking back from a world saturated with CGI (a lot of which still has a lot of flaws and I still don't prefer), the prequels are actually pretty impressive visually on that score.

2) Too much filler story - the product of Lucas with total creative control - cut out many, many minutes of slow exposition and Pe/Anakin love story and you get better movies. Clones can be cut down to an hour 20 and it would be a great movie. You wouldn't even have to cut the hokey droid factory to make it great. Everything after that scene in the movie is actually amazingly awesome.

3) Sith is a great movie no matter how you look at it - and a great exposition of Vader's origin. Forget the fan service of the sequels, this was wonderfully managed and satisfying.

4) Personally, I loved the big political arc of how the democracy was lost and the emperor took control. It just needed to be told with a writer like Kasdan on board - again a case where Lucas had a bit too much control. He brought an amazingly powerful story arc, like the Star Wars themes of good v evil and the Skywalker bildungsroman, but this angle lost a lot due to less polished storytelling.