Have you considered, based on the theatrical trailer, that perhaps it is not a MWAM defined by the machines having control, but in fact a level of control defined by another level of entities "GOD" if you will??? So therefore the machines and the humans are controlled...sort of alluded by the council member guy to neo when they were looking at the control room downstairs in zion...who needs who? Why exist at all? Perhaps neo gains an ability to see the real world like he sees the amtrix...at a level beyond ordinary comprehension...thus the golden corridor, the tenticles foing throught him...maybe the blindfold is to aid him in this sight...perhaps neo realises that machines have souls too? In that end, machines and humans are only seperated by the materials they are constructed with...
Then again it could all be a hell of a lot simpler than this, and most other theories put forth...just could be a really funky action sci fi flick....yadda yadda man machine battle shake hands agree to disagree lets go start a new human eden (zion????) on the surface neo bags first goes at trinity blue sky on mars ...the end