The second movie has me pretty convinced that the humans are still inside the matrix, even within Zion (matrix within a matrix). As evidence of the fact I turn to 1) Smith leaving the matrix, 2) Neo being able to sense the machines on the 'outside', and 3) the Architect's discussion with Neo. The architect basically tells Neo the same thing that Smith told Morpheus in the first movie, except he adds yet one more incarnation of the matrix to the story. The architect implies that event he 20th century earth version failed and they had to build a third one. Basically they had to build a matrix where there was 'something more' beyond the 20th century earth. I think that Hamann is most likely an AI construct, and was never noticed by Neo before because for some reason Neo wasn't able to notice he was in an 'outer matrix' prior to his discussion with the architect. The point being, there is no need for cyborg's etc.. no security in Zion would protect it because it is programmed that way. Hamann would simply be another part of the programming.
The interesting question then actually is the same question from the first movie, which is: "what is the matrix?" The fact that the world of Zion is still a matrix brings into question all of the history we've seen in the movies, as well as the "Animatrix". In other words, it could all be a lie. Frankly, one of the things that always disturbed me about the first movie is the scientific flaw of using humans for energy when there is no sunlight, because they never really deal with the problem of where they get the energy to keep the humans alive. Granted this is science fiction, but even science fiction generally tries to stay within the bounds of real science as much as possible.
So the question is why are the machines keeping humans alive? Or even better, are there any humans at all? Perhaps the whole thing is a giant program. One of my own theories is that humans built the matrix in order to escape some post-apocolypic scenario and programmed the machines to create a paradise for them. That failed, and the machines are now simply doing their best to comply with their programming. I feel that a theory along those lines goes along with what the oracle says. However, it is merely conjecture.
i am the biggest proponent of MWAM (matrix within a Matrix) however there are flaws in your thinking...
1) Smith could leave the matrix either way...If zion wasn't a matrix, then it would be the same thing as changing the OS on your computer, remotely...its possible, but it doesnt happen often.
2) the use of humans to create energy is feasible, although it wont be done in our lifetime (thank neo), however, they do not put ENERGY into the humans, they FEED them, thus using our own natural processes against us, so to speak. The humans are being kept in a conrtrolled environment, asleep, so they are basically just chemical processors, taking sustenance and producing energy "which, when combined with a form of FUSION, provides all the energy they'll ever need"
i think a MWAM would be cool. but the only thing i wonder is how would it all end. I (hopefully we) care for the characters in the story very much. I would be kind of disappointed to see them all poof disappear end of story because they were programs themselves. I think the idea of a WMAM would make a better stand alone movie, rather than a trilogy. unless i am just not fully understanding this WMAM concept.
but why would he (meaning hamann the previous one) want to keep up the prophecy? If he knew what was to come, he would tell Neo, in the hopes that neo would be able to stop the cycle. Also, something i just remembered...If Hamann WERE the previous one, why would he NOT know how Neo "does the things he does"? If he were the previous one, he would not only know how Neo can do them, but he would be able to do them himself.