Midi-chlorians were not there “since the first draft.” And over-explaining everything is not the only way to tell an “intelligent” story.
Are you sure? Weren’t they at least there early on, if not the first draft?
No. Funny enough, this was just discussed on the site very recently: https://originaltrilogy.com/topic/Proof-of-Lucas-revisionism-in-Rinzlers-making-of-book/id/66017
I don’t think Midi-Chlorians are an over explanation. I think they enrich our understanding of the Force. Plus if Lucas was able to make the sequel trilogy, then they also serve as a setup.
The argument is that the force represents, amongst other things, life itself. To explore so deeply as you want the literal “what” and “how” and “why” of the force would be like asking for the film to give a definitive meaning of life. The force was designed as a mystical energy that is inherently unknowable. It is up to the characters to decide what to do with it and how they will use, much as it is up to them to decide what they will do will their lives and what choices they will make (and, of course, which side to be on). To pin down what the force is would be to simplify and demystify it.
Personally, I don’t have as big an issue with the midichlorians as presented in the PT as many do (though I don’t love it). But I would not be okay with what you seem to have wanted (and what Lucas debatable would or would not have done), which would have been to take the explaining to a whole other level.