Midichlorians never bothered me. I don't mind scientific explaination for mystical acts. To me, its not a denial of; more of a reason how.
But Jar-Jar Binks and his bumbling, walking plot device of a racial cariciture even existing makes me vomit. I definitely headcannon his scenes. Same for the podracing scene in episode I.
@JamesKM716: But honestly, EU novels are some of the best stuff I'v read, especially the Legacy of the Force and The Fate of the Jedi series. You should check them out if you haven't read them. (But to understand everything, you need to read everything before it.)