I thought the reason the machines have to use humans was simply explained in the first movie: We're all they had left. After the humans scorched the sky, any lifeform on the planet that was not extremely intelligent and adaptive would die off rather quickly. I.e. No sun=no grass. No grass=cows die. If there WERE any cows, we wouldn't have had the Cypher problem because he would have more to eat than the gooberslop on the Nebuchadnezzar and he wouldn't have to go back into the Matrix to get juicy and delicious steak!
On the other hand, there may be a surprise revealed in Revolutions as to the real reason. For example, what if the Matrix was an idea created by a human in order to save the race?? Then Neo is really the bad guy. It would make for a cool ending, dontchathink?