He introduced midichlorians to illustrate the advanced enlightened society of the past, dominated by science and knowledge, in contrast to the dark ages rooted in mysticism of the original trilogy. It makes sense on paper and is a good trope to work with, the problem is that the prequels take place what, 18 years before the OT? The very idea that all this great super-industrial society and all its knowledge would just collapse into the rugged world of the original trilogy under any circumstances in just 20 years is ridiculous. The two concept of the force - mystical one one and academical one - taking place so close to one another, clash dramatically. The fact that there's no pay off, except purely retroactive, doesn't help either. What he should have done instead is set the prequels thousands years into the past, maybe even making them anthological, depicting the first seeds and the slow subsequent decline of that advanced society over several generations, Asimov style, leading into the world we know from the OT. You can still have Jedi swinging the lightsabers. That way, the revelation that the force was once, to an ancient civilization, a scientific subject would be just as intriguing as the mystical force we were introduced to, rather than basically substituting the OT force with midichlorians and whoever has more of them wins by default.
But then we wouldn't have all the embarrassing pottery linking literally every single event of the prequels to the original trilogy as if a college student wrote it. Lucas is the idea guy, he shouldn't write scripts.