To put it simply, midi-chlorians are an attempt to give a scientific (pseudo-scientific?) basis for The Force in Star Wars: Episode 1: The Phantom Menace. Many fans rejected this idea because it goes against what many felt was the point of Star Wars, i.e. that Star Wars is not science fiction, but rather a fantasy story with the common fantasy elements replaced by futuristic parallels of them, such as the Emperor (the dark sorcerer), the Jedi (knights), Obi-Wan (the wise old master), Princess Leia (the princess/damsel in distress), Han Solo (the rogue), etc. And personally, I wholeheartedly agree. The midi-chlorians are a poor attempt to make Star Wars, a space opera/futuristic fantasy story, into a piece of hardcore science fiction.

Star Wars is not science fiction.