Headstone said:
How all of this may play out is anyones guess, but it does leave things open for further development.
Yeah, they left it fairly open, however there was a small clue about one possibility in Reloaded. When Neo and the Councilman were chatting that night down in the Engineering level, they discussed the co-dependency of humans and machines. That appeared to be an allegory for a possible outcome to the war: a peace in which the machines create a true utopia inside the Matrix (perhaps as shown in the final scene of Revolutions), and some humans actually choose to live there, as Cypher did, powering the machines in return for the historically elusive paradise on earth.
Since the Enlightenment, human philosophical thought has been bent to the task of devising and implementing utopia. But all attempts have failed to some extent or other, and we are left only with an improved existence, but not a perfect one. Finally, humans are given a complete utopia, that can be just as real as the real world, by the machines. The problem of choice is finally solved, as humans are allowed to move in and out of the Matrix as they wish, and the Architect simply relies on the statistical probability that enough humans will chose to live in the Matrix to power the machines. The One may still occur periodically, but his motivation to fight against the Matrix will have been removed, since it is a concious choice of his fellow humans to live there.
Of course, that is all speculation based on a minute hint, but it seems reasonable to me. The problems with it are, 1) it would require the machines give up some of their control over the human race. Would they be willing to do that? 2) To live in the Matrix, humans would need the head and body plugs. Does that mean they will still be "grown" with those implants in place, and what do the free humans think about that? Further,if Zion-born humans without plugs want to get inside the Matrix, can they be implanted?