I agree. A better premise would have been that the humans had done something to make it very difficult for the machines to create other sentient machines and so they needed to tap the brain power of the humans to do the calculations necessary to find a way to get off the planet.
That would still be a stretch, but not quite as silly as humans as batteries.
That's an outstanding idea. They could even have found a way to make dreams a part of that scenario.. Maybe they could explain the "I did not finish my school and can't find the class I am supposed to be in" dream, or the "I can't quite reach that thing I am trying to grab, even though it's right in front of me" dream. Maybe those dreams are just part of the space-time travel iterative calculations that do not converge.
So perhaps a re-make is in order where the silliness of the second and third parts of the story are abandoned and the replaced with the second part being about NEO leading the human race to near annihilation of the machines (as promised in the the original), and the third part being that NEO discovers that the machines want to leave earth. Then he has to redirect the efforts of the humans, who have by now been taken over by democrats who want to reinstate the matrix as a utopian paradise, to assist the machines to leave earth and travel the stars as our ambassadors with the promise they will report back if they find any habitable planets.