Midiclorians and Jar Jar are not what is wrong with Episode I. Sure Jar Jar is annoying to adults, but kids at the time actually probably enjoyed the character and thought he was funny, that was his intended purpose. You have the mind of an adult, not the mind of a child and you have mostly forgotten what its like to have a mind of a child. Whether you agree with the timeline they started with or not, Jar Jar played an essential role in episode I by bringing the Gungans and the Humans on Naboo together. He also is the person who gave Chancellor Palpatine his emergency powers (as you mentioned). I will concede they could have gave him those powers in multiple different ways, but at that point Jar Jar was only on screen for a few seconds in the last 2 Episodes.
As far as Midiclorians are concerned, I'm perfectly fine with the explanation. What makes one person stronger in the force than another? If this was never explained then fans would probably be complaining now that we don't have an explanation. Had Lucas not sold his company, we probably would have even more information at this point about how the force works. There is something much deeper about the force that we will never get to know now that Lucas is gone. Maybe that makes you happy, but I and many other fans think it stinks.
I dont care about Greedo, and who shot first. If i had a preference then it would be the way it was originally shot. But it doesn't really change the films, and you got to see it in its original form so whats the difference anyways. Its clear that Lucas's best days of directing and writing dialogue are behind him, that wasn't his strength anyways. His strength was telling a story, and he still has that ability and Disney would be fools to not involved him somehow in their projects. I'm fine with him staying away from the new trilogy, but i would bring him in for a spin off, or the animated stuff.
Lastly, the reason you look at Star Wars different now than you did back then is that you are a jaded adult. I don't mean that as an insult, it happens to all of us. You are looking at it through different eyes. You are much smarter and wiser now and its harder to suspend belief and not nitpick and just enjoy the movie. From what you say it sounds like you wanted more of the clone wars, and that was what the animated series was all about. It showed the hero that Anakin Skywalker was, and the good man that he use to be. You only get so many minutes in a movie and it can't tell the story that a TV show can. Lucas wanted to show the downfall of Skywalker and the downfall of the Jedi order, and I think he did a pretty good job. I just shut off the really analytical side of my brain and enjoy it, like a child would.
I think a lot of what you says has merit regarding the mind of a child vs. the mind of an adult. If anything, however, I think I admire the original trilogy even more. Maybe that was because the prequels were so bad that it made me love the originals even more. Maybe it is just sentimentality, though I readily admit the originals aren't perfect - for example, in Return of the Jedi, I'll readily admit that Mark Hamill and Ian McDiarmid were the only ones who bothered to show up and act. I mean, to me, the late 70s/early 80s were the best years of my life and maybe to some extent, I still have those rose colored glasses on.
But I still disagree that showing things like midichlorians added anything to the story. Heck, Lucas even stretched or completely ignored his own established canon with the prequels and that still rubs a lot of us the wrong way:
1. IIRC, Owen was Kenobi's brother in the SW novelization.
2. The battle between Vader and Kenobi in which Kenobi defeats Vader was slightly different; I can live with the way it was depicted but I think it could've been better and Obi-Wan certainly didn't try to dissuade Anakin very strongly:
RotJ novelization:
Kenobi: “When I saw what has become of him, I tried to dissuade him, to draw him back from the dark side. We fought … your father fell into a molten pit. When your father clawed his way out of that fiery pool, the change had been burned into him forever–he was Darth Vader., without a trace of Anakin Skywalker. Irredeemably dark. Scarred. Kept alive only by machinery and his own black will …”
3. From the movie:
Kenobi: "Luke, you're going to find that many of the truths we cling to depend greatly on our own point of view. Anakin was a good friend. When I first met him,
your father was already a great pilot. But I was amazed how strongly the Force was with him. I took it upon myself to train him as a Jedi. I thought that I could instruct him just as well as Yoda. I was wrong. "
A great pilot? Uh, what? A 9 year-old kid is a "great pilot?" To try to meet this, Lucas threw in the lame pod racing scheme and then had Anakin bumble his way to the droid control ship in a Naboo Starfighter, luck his way into destroying it, and then flying back.