Now let me start by saying that I was quite young when I first saw Menåce des los Phantasms, but at the time the concept of midi-chlorians didn't really have an effect on me. I was old enough to understand it logically (to the extent that there is logic to be teased out from Qui-Gon's somewhat feeble explanation), but I guess I wasn't yet at the age where one needs to actively seek out wonder and mystery in the world.
Now that I'm a little older and wiser and jadeder, I believe I can understand some fan's ire at the concept of trying to explain a mystical and omniscient force away with microscopic organisms (though ironically if you turn that around, you get religion). It still has never got to me though. I agree that the midi-chlorians explanation is kind of lame, but it is also so hand-wavy that I find it impossible to be particularly disillusioned by it. In my opinion, the whole thing speaks to how quick we are to assume something is understood once we have applied a name to it. How does the force work? Midi-chlorians. Why do things fall? Gravity. Why am I afraid of chopsticks? Consecotaleophobia. How are the Rolling Stones still performing? Spackle. You get my drift.
The truth is that midi-chlorians explain practically nothing about the Force, they just raise more questions. Why do microscopic organisms in my blood allow me to send an object flying across the room? Do they send a telegram to it's molecules in the preferred format, politely requesting a relocation? Do they fly out of my hand in an invisible cloud and manually carry the object away? Do they all just wish really hard? No, I'll tell you how it works: Magic. The same way it has always worked.
Now I guess Lucas wanted to use midi-chlorians partly as a plot device, so he could explain why Qui-Gon was so insistent on bringing Anakin along, and also so he could explain Anakin's divine conception without getting sued by that guy who wrote the Bible. Personally though, I feel that the whole thing would have been better and more interesting if he'd instead had a conversation with Obi-Wan that paralleled and foreshadowed Vaders ominous talk with the Emporor in Strike-Back des los Impériosøs.
OBI-WAN: What is thy bidding, my master?
QUI-GON: There is a great disturbance in the Force.
OBI-WAN: I have felt it.
QUI-GON: I just met some kid -- Anakin Skywalker.
OBI-WAN: Yes, my master.
QUI-GON: He can race pods.
OBI-WAN: He's just a boy. I disbelieve his ability to race pods.
QUI-GON: The Force is strong with him. I totally believe he can race pods.
OBI-WAN: If he could be made a Jedi, he would become a powerful ally.
QUI-GON: Yes. Yes. He would be a great asset. Can it be done?
OBI-WAN: He will join us or else have to make Jingle All the Way 2, my master.