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Originally posted by Botnst
The guy said he was trying to establish a world that was both complete and consistent (which is extremely cool and violating a math theorem (Cantor?) that indicates that impossibility). Anyway, he indicates that he has been refining the matrix through an iterative series of approximations, each more stable than the previous.
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I'm not sure if this is different from what you're saying or not (not sure what you mean by "iterative series of approximations"), but I thought the conversation indicated that there were five or six previous versions of the Matrix, each with its own Neo/Zion, and each time, the information gleaned from that Neo's experience was used to further refine the next version of the Matrix. Also, that Zion + the "Prophecy" provided a predetermined escape program for those individuals that rejected the confines of the Matrix.
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With Star Trek logic, saving the many is better than the saving the one--which Neo violates by choosing the irrational--proving that the Core could still not predict Neo; that the Core had not yet produced a complete and consistent matrix, that Neo's free-will choice could still defeat the machine logic.
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I think in this case, the Architect had already predicted that Neo would choose Trinity over Zion - hence the statement "But we already know what you are going to do. Already I can see the chemical precursors..." In this case, they would now be able to destroy Zion for once and all, but I'm not sure what it would get them because it seemed like a pretty good system to me.
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The coolest hint at who Neo is, came in the last scene: remember it?
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You think he's Smith?