(I didn't post this on the F&D Beta boards, since the topic seemed to pertain to all SW, but I might be wrong.)
There seems to be a tacit consensus that midi-chlorians were a huge mistake on the part of George Lucas, usually listed next to Jar Jar Binks in a list of stuff the prequels ruined.
I'll admit that I grew up on the prequels, and despite the fact even my young artistically-challenged self could see the bad acting and lackluster rythm of the likes of AotC, I can't resist enjoying them. In fact, looking back, the senate/political scenes and Padme arcs are something I prefer in the prequels to the scarcity of scenes showing the Rebel Alliance command.
But I disgress. Since I grew up always "aware" of midi-chlorians, I never felt their introduction to canon was removing the magic / mystique / mystery / spirituality of the Force. Maybe it's just me, but the fact that living creatures similar to mitochondria played a "relay" role between the Force and living beings never seemed out of place. On the contrary I found the "whole living beings within living beings" to be quite full of taste.
I've read in a few places that midi-chlorians brought too much of a Hard SF feel to the more romantic/fantasy Star Wars world. In my experience of old pulp SF novels, the lines were not always so clear cut, and technobabble was often a mean to raise philosophical/ethical questions, advance a particular storyline or stimulate the imagination; not necessarily have a "science talk".
I'm curious to hear other people's take on the matter, especially of those who have either downplayed their role in their games, eliminated them completely, or else. Unless I'm mistaken, there is (almost?) no mention of them in the FFG books, which can be understandable in the context of the Galactic Civil War.