My biggest problem with the prequels is that they severely lack any sound character motivation. That is entirely the fault of Lucas as writer. The writers he brought in for Ep 2 and 3 should have fixed that. The prequels feel like very rough, early drafts or even outlines of a movie. But he never fleshed out his ideas enough to tie the events together. Yes, Anakin and Padme are supposed to fall in love, but they never showed why or how they did. In fact, what he did show would really have forced Padme to put out a restraining order on creepy Anakin. You have to show the audience how something like falling in love happens instead of forcing the audience to simply accept it. Sure, I can see why Anakin likes Padme. But why would Padme ever like him back? He hasn't shown any redeeming values at all to her, only that he complains and blames everyone else for his problems, and is a homicidal maniac with anger issues. And Padme really likes this? It's not even like Anakin is a bad *** bad boy with a motorcycle and Padme's trying to piss off her parents. The only thing Anakin ever showed Padme is his obsessive attraction to her. It's as if Padme has never had any boy ever like her (except for her first time when she was twelve) and she's really desperate.
I also think the prequels would play better with 80% of the dialogue taken out. If you don't hear any of Anakin's repulsive dialogue when he's trying to woo Padme, you might be more inclined to accept their courtship.
Oh, and the terrible attempts at humor. Terrible terrible. So embarrassing. And so unfunny.
Pixar has shown (at least prior to Cars 2) that it can successfully write a movie aimed at kids with a lot of wit, insight, excitement, and most importantly, heart. Those things are universal and appeal to every age group. So it is possible to do.
Anyway, visually they are still interesting movies and I enjoy most of the action sequences. I have most, if not all, of the "making of" books because I love the artwork and designs, and I have the PT on DVD (but didn't get the Blu Rays). I mostly collect the OT stuff, but I have a couple of figures from the PT (Ep 3 Obi and Ani) and will get Grievous as well. So I'm not a complete PT hater and can appreciate it for some things.