seeing that i missed the last couple of minutes of the movie and since i had nothing better to do, i went to watch it again yesterday.
while watching the movie some of the ideas that were presented in this thread were running thru my head, this gave the movie a whole new perspective. the ending made the theory of a second matrix sound possible seeing how neo felt the sentinels comming and then stopped them.
but then something poped into my head, agent smith said that their was a connection between them maybe they have a part of each other in the them (when neo destroyed smith in the first part or maybe when smith tried to transform neo before the fight scene) now if i\'m not mistaken, agents are able to communicate with the machines.
now if neo has a part of smith in him that would give him some of the agents powers right, thus giving him some control over the sentinels their by stopping them.
sorry if it sounds distorted (and most probably flawed) but i cant think of another way to put it right now.