I can sum up my biggest problem with the prequels (well, with Lucas really) in one word: midichlorians.
When he decided to explain how the force works, he took something that had been so eloquently portrayed in the OT*, and reduced it to something banal and mechanical. And there was no reason to do that. It's not like Darth Vader needed a blood sample to know that Obi-Wan was on the Death Star. And yet Lucas chose to do it anyway.
That choice showed such a baffling level of cluelessness. Like here's this guy, this supposed visionary, who has carte blanche to do whatever he wants (with what is supposedly his own story, no less) and he just.. doesn't really seem to get it?
It really made me question whether the OT were as a good as they were because of him or in spite of him. Apparently I got something out of the story that he did not.
* I'm referring particularly to Yoda's speech to Luke about the force in ESB. "Luminous beings are we, not this crude matter!". Beautiful writing, still gives me goosebumps. No wonder ESB is often considered the best one.