I'm in the very small minority of people who liked the prequels. I grew up in the 70s and 80s, so I saw the original trilogy in theatres. I grew up with all the Star Wars toys.
Yes, TPM bothered me the first time I saw it in '99. Jar Jar particularly. But, over time as I've seen it more and more and shared it with my son as he became old enough to understand Star Wars I came to like all of the prequels. TPM is my least favorite of the three, followed by Attack of the Clones and then finally Revenge. Sure there are irritating parts (Jar Jar again, Anikid, Hayden's whining), but there are also some very poignant parts--Anakin killing the sand people while Qui-Gon impotently yells "No" from beyond, the final conversation between Obi-Wan and Anakin after their battle on Mustafar, etc. These are the hints of the deeper characters that we don't always get to see.
As for the "midichlorians", this concept never really bothered me much either. I've always thought of this as a sci-fi re-imaging of mitochondria. After all, we all have organelles living in our cells which carry their own DNA, and by one scientific theory were independent single-celled lifeforms that became symbiotic with other single-celled organisms which eventually evolved into eukaryotic cells. Why is it unfathomable in an sci-fi setting to conclude that one's mitochondria can give a segment of the population special powers? After all, if you can sense and manipulate things at a cellular level, you can certainly work all of the magic that a Jedi/Sith does.
Did George Lucas do everything right? Certainly not. Were there mistakes? Absolutely. Would I have done things differently? Most certainly*. In the end though, perhaps I'm just a Lucas apologist. But, I do have very high hopes that JJ Abrams handles the reins in a more responsible fashion than George did.
* think about how awesome the story line would have been if it were revealed in the prequels that Anakin's turning to the dark side was an elaborate plot by Obi-Wan, Yoda, and Anakin to get an agent close to Sidious in an effort to overthrow him. Squandered opportunities.