When the Nebbachunezza was destroyed by the Sentienls and they were fleeing through the tunnels, Neo stops and mentions that he can "feel" them. Then he unleashes his own electromagnetic pulse and disables the machines. My guess is that Neo has synchronized himself even moreso with the Matrix, to the point where he can extend his influence over the machines that are controlled by the Matrix's programs in the real world. That's what I figured when I saw it, anyways.
About the confrontation with the Architect. From what I gathered, your statement makes sense, but I don't understand why the Machines would be fostering resistance to their own power supplies by permitting another Zion to form again and again. Perhaps they have no control over that. From the sounds of things, the Matrix is somewhat like a giant, mathematical algorithim, with point-blank, black-and-white equations which, when you plug in the imperfect human minds as your y's and x's, creates an unbalanced equation that humans are able to reject, given the prospect of mental comprehension (choice), and thus causing system errors and loopholes to seperate from the mainframe. Perhaps escaping humans is inevitable and so they use the aforementioned cycle of "Ones" to maintain an equilibrium of sorts; Zion repopulates, resistance grows tense, and the One unwittingly stiffles it. Thus, the friendly Oracle, despite her good intentions (the result of AI processing choices free of the system), could be a control herself, unknowningly mired by the program bearing over the environment (the Matrix). In that case, there really would be no messiah, so to speak.
And exactly how will Neo free all of the humans in Revolutions? It sounds like freeing any more then twenty-three humans, half of which are male and the other female, will trigger a massive system failure that'll terminate humanity. Then Earth will be left to the Machines. Even if Neo does shut down the Matrix and escape with twenty-three humans, they won't stand a chance against the Machines back in the real world when they resort to their back-up energy sources. Seems like a lose-lose situation to me...
Confusing sh*t, this is.