1) If it's only midichlorians keeping the vast majority of sentient life forms from being Force users, you'd think that they would be able to figure out how to make them. They already had cloning technology . . . 2) My main issue with midichlorians isn't an argument for religion. It's an argument of changing what was established as a philosophical (as opposed to religious)discussion and undermining with an explanation that isn't necessary. Besides the fancy tricks the heroes and villians can do with the Force (lighting, telekinesis, mind control, et cetera), the main role of the Force is to divide the heroes and villains by assigning them as either light and dark. Since midichlorians doesn't add anything to that aspect, what's the point? 3) Midichlorians as violation of the rule on Chekhov's Gun... Chekhov's gun is a dramatic principle that requires every element in a narrative be necessary and irreplaceable, and that everything else be removed.
"If in the first act you have hung a pistol on the wall, then in the following one it should be fired. Otherwise don't put it there." Anton Chekhov
If we removed all references to midichlorians from the movies, would any of the movies suffer? Nope. If the presence or absence of an explanation how the Force works isn't important to the story, then why bother to include it?