well, maybe that equation is still unbalanced (the whole reason why neo existed in the first place). i'm not sure it really had to do with the war, but with the nature of the matrix itself. i mean, the architect didn't say he was there to stop the war, just that he was the remainder of an equation.

i can't really remember, but at the end, was it said that all the humans in the fields would be unplugged? i don't think so. which is interesting.