I am in the minority, but i thought the prequels were pretty good for what they were. The hype especially for the first one was so high that it never was going to meet it. They did suffer from a couple problems though...
1) Lucas relied a bit too much on CGI effects for the prequels.
2) It is hard to buy that Anakin Skywalker is that awesome at age what 5 or 6 in the first movie. Especially when he takes about being able to pod racers---hell, he could barely see over the dashboard. If you make him 7 or 8 that is a lot more believable.
3) The problem of trying to do everything at the speed of light just to cram it into 3 movies. Episodes 4-6 covers what 5-6 year period? Whereas the prequels cover 15-20 years.That is a lot of ground to cover.