OK, i've been hearing a lot of this "when Smith assimilated Neo the machines unplugged him/corrected the program(Smith), and that's how Smith died." There is a huge plothole in that. Smith had taken over hundreds of humans hardwired to their system, so they could have fixed it in the exact same way using one of them.
Some other (not-so) quick things -
I think the whole explanation of Neo's vision and powers of machines in the real world is quite hollow. He was connected to the source, so he could see and control sentinels? Huh? Since when can machines modify a human mind, incidentally, to give it metaphysical (ESP-like) powers? Since when were human minds capable of such things ("ESP") in the first place?
Why in gods name did the machines keep their word to the now incapacitated/dead/whatever he might be Neo? Why would they reveal the truth of the matrix ("the ones who want to be freed" - Archie) and then actually free them ("they will be freed" - Archie.) Perhaps they found a new power source?
I have tons more to say but that's enough for now. Just a non-plot related comment -
Did anyone think the new Oracle was really lacking, and this movie was missing alot without her? Did anyone find it ironic (as sad as it might be) that she died of diabetic complications, and in the movies she's all "I LOVE cookies", "I LOVE candy"?
Smith was defeated because Neo allowed him to infect him. That created a connection between Neo and the billions of other Smiths. The machines then sent a pulse or antivirus into Neo, thus affecting the Smith that had taken over Neo. Because of the connection to every other Smith, the antivirus spread throughout them, freeing everyone that Smith had taken over.
__________________ "The MTV Movie Awards are a systemic anomaly inherent to the programming of the Matrix. Although the transport process has altered your consciousness, you irrevocably remain human. Ergo, concordantly, vis-a-vis... You know what? I have no idea what the hell I'm saying. I just thought it would make me sound cool."
-The Architect AKA Larry