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Hmm, great posts so far in this thread. I someone MUST have hit upon the true answer to the riddle. A few points that I have that no one seems to have brought up that reenforce some of the points made here:
Agent Smith tells himself "It's happening exactly as it happened before" replies to himself "Well not exactly".
Now if we imagine the Matrix trilogy to have an ending that gives the struggle purpose we have to assume that something is different about the struggle this time as opposed to 5 others the architect mentioned (seems reasonable enough to believe him to an extent). This goes well with the theory of Smith being a virus and a spoiler. Though evil he has been serving a purpose in changing some of the events that should have transpired. No DOUBT that it is Smith in Bane's body there.
I also agree with the Matrix in a Matrix idea. We have never seen the real world, and perhaps in attempting to save Zion now we will get our first glimpse of it. It may be damaged as it appears now or perhaps look totally different. One can never tell. I disagree with Neo being anything less than human. This is a big Star Trek thing. Emotion and Humanity being the only things that matter.
So we are left to realize that enitites like Mero and Smith have seen this sequence of events before albeit slightly differently. Why was Smith waiting for Neo? He wanted to gain entry himself. He wanted power and control. He now has free choice, as do Neo and now his entire enterouge. Freed of the idea of the prophecy and having to do everything to reach that point they are now operating of their own free will.
BTW, mainframe codes to Zion. Sure it SEEMS like the agents wanted them, but remember it is preordained that they will never get them. The one has to be given a choice to save Zion or not to reset the program.
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