This is true, but bear in mind that he had absolute, total control and final say over every creative decision over all five of his Star Wars movies after Star Wars '77. They've always represented his vision more than any one individual, no matter how many revisionist, baseless theories about Kasdan, Kurtz or Kershner being the secret unsung talent behind their respective works. I will give Marcia Lucas a big hand, though. The prequels could definitely have benefited from her contribution, unlikely as it was.
If anything, subsequent views of TFA actually grew on me. I walked out of the theater feeling conflicted, but have warmed to home viewings since, even though I still think it's sub-par as a Star Wars film. My viewings of Lucas' Star Wars movies over the last 35 years always, without condition, conjure up feelings of elation and awe.
TFA can't do that.
Not really. You can view Midi-chlorians as stuff Obi-Wan simply left out when he was telling Luke about the Force, but they don't actually contradict anything he says. The Force is still an energy field in the Prequels, just as Obi-Wan describes, and it's interacted in with the same way. It's just that those who are Force-sensitive have these little microscopic critters in their blood, channelling that energy.
Well the Jedi are really into the Force, so it doesn't surprise me that they'd have some method of measuring it, or understanding it better than others. My take is that Qui-Gon realised Anakin's Force ability was abnormally powerful and wanted to know if there was something 'wrong' with him (which of course there was). I think that's basically the only reason for their existence in TPM, and possibly also promoting the idea that we interact with the Force at a biological level rather than a wishy-washy 'magical' one.