As someone who does not hate the Prequels I may have a unique perspective on them.
First, it must be said that the PT are not as good as the OT. Lucas knew that going in. So there is that which causes a lot of people to complain about them. Second, Lucas wrote and directed each of them himself. He did have some help credited on Attack of the Clones, but that is the weak point of the PT so the other writer didn't help. Third, Lucas had a very singular vision of what he wanted the story to be. I find that he was too covert in some of his story telling. He should have made it more obvious that Palpatine and Sidious are one and the same and that both the blockade of Naboo and the Clone War were just grand ploys to gain power. The trilogy is about the rise of Palpatine and the fall of Anakin and the Jedi. The story just is not clear on the surface. Too many things are done very subtly. It hides the real story and hurts the story arc.
I've noticed other things. Everything about the PT is based on typical 30's and 40's story telling. It didn't go over well for the modern audience. The comic relief is too in your face. Jar Jar in TPM and C-3PO in the droid factory in ATOC. And the relationship between Anakin and Obi-wan in ATOC is too confrontational and you don't get the sense of a friendship there. Anakin chafes too much at Obi-wan. It would have worked better if he was chaffing at the Jedi Order and Obi-wan was more understanding and friendly about it. And these movies show Lucas's weakness in directing actors. He managed it for THX, American Graffiti and Star Wars, but seemed to have fogotten all his directing skills. After watching Hayden's performance many times I figured out that Lucas made him talk like James Earl Jones. If you lower his voice the phrasing matches but he sounds like a moron. A small piece of how he comes across is his own acting skills, but 90% is trying to talk like Darth Vader. A different actor may have pulled it off better. It is rumored that Leonardo DiCaprio was up for the role and he probably would have done better (he certainly would have looked more like Jake Lloyd and Sebastian Shaw).
So pretty much all of the failings I lay at Lucas's feet for the bad execution of what could have been a great story. I enjoy the films (except for the droid factory scene in AOTC), but they fall short of where they could have been.
The other aspect that I see with some franchise movies lies with fan expectation. When fans expect a certain thing and they get something else, many don't react well. Many often don't realize their dislike lies in their own expectations and they try to find someone else to blame. So the actors get blamed, the CG gets blamed (the PT actually had a great deal of practical effects and most of the CG is matte paintings and digital compositing.
What is perhaps the most annoying is that the OT didn't need a special edition and the PT does. But then Lucas never fixed the most blatant errors in the OT for the special edition. But a lot of the issues are unfixable. Jar Jar Binks is fixable by redubbing him in another language (the fan edit I saw used the Hindi language track for Jar Jar). He becomes exponentially less annoying and you don't even have to change the dialog, just subtitle him.
