I loved the prequels so the stuff I didn't like would be the shorter list.
As zombie said, a lot of plot points set up for resolution in ROTS aren't really dealt with. The Sifo Dyas thing, vanishing/immortal Jedi and probably a few others. The theory is that Lucas was already overburdened with plot points and stuff so he just left those things out. I see no reason to doubt that either but that doesn't mean I have to like it.
One thing I did like was the spectacle and the scope of the visuals, particularly in Episode I. I've always loved the podrace, the arrival on Coruscant, all of Theed and Naboo, etc. Amazing visuals, imo.
One thing I dug was the visual transformation that took place over the series of the films. The production design, costumes, etc, all slowly transitioned over from more organic, individualized, hand-crafted types of production to the more machined, pre-fab type of look.