I actually didn't care for The Phantom Menace too much. I'm just a casual Star Wars fans so I come from a different angle I guess. However, Darth Maul was a great villain. I was disappointed he was killed off. Since Anakin didn't become Vader until the 3rd film they could have easily kept Darth Maul at least to the 2nd film. Jar Jar Binks, well, the less said the better. Frankly he's part of the reason I can't get into TPM.
Attack of the Clones and Revenge of the Sith were ok, but could have been better. I actually loved Natalie Portman as Padme (I'll admit, part of that is because she's beautiful and I am a sucker for a beautiful women

) but I thought she did well. She wasn't some maiden that needed to be rescued every minute, she was perfectly fine with picking up a weapon and taking on the enemy herself. But what's his face (I don't feel like looking it up) that played Anakin, he was brooding way to much. And there was little to no chemistry between him and Portman. I'll give them the benefit of the doubt in the sense that I think they were trying, but sometimes either it's there or it isn't.
I get what Lucas was trying to do with centering the story on Anakin. After all, it's his betrayal that really brings the Republic down. If he had gotten a better actor---or at least an actor that better fit the role, I think they would have been better. By the time ROTS came out Lucas sort of had to go into fast forward because by the end it had to lead into the first Star Wars film and we were still pretty far removed from that by the end of AOTC. I actually liked Palpatine in ROTS, in the first 2 films he was sort of meh. But in ROTS he finally took that final step to becoming the evil Emperor we all know and love.
So I think the prequels are a missed opportunity in a lot of ways. There were some things I liked but they never developed to their full potential. They were always going to pay lip service to fans, after all they were prequels and they had to develop into what we know was the original trilogy. I don't think that was the problem. I think Lucas got so wrapped up in the special effects end of things, he lost some of the character development that made his first trilogy so good. And while I agree Anakin was probably the right choice to center the trilogy around, he took too long to develop that angle, and the ultimate reason for his turning evil just didn't jive all that well to me.
One little ingenious bit I did like from Lucas was in TPM when Qui-Gon was convinced Anakin would destroy the Sith. He was absolutely right. He just didn't realize the years of hell that would happen in between. But yes Anakim would eventually defeat the Emperor.