Extracting every solider you knock out would be ridiculously tedious. You'd have to carry them far away enough not to alert the entire base, extract them, go back and then do it all over again. I understand that some people think the Fulton system is too unrealistic (Come on though, this is Metal Gear) but I think it's important to suspend disbelief for these kinds of systems that will make playing the game more entertaining and less of a chore.
But you can load people up in a vehicle, so it wouldn't be quite as tedious as carrying them one at a time.