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The one thing that most people seem to be forgetting or overlooking is that the ideas presented in Reloaded make the reasoning in the first Matrix movie obsolete. Using the supposition that the "Real World" and Zion are infact another martix (which seems to be the common consensus), this means that everything that Morpheous tells Neo about the machines, the war, the energy source, and the matrix itself are concepts that exist only in this new matrix, created by an even higher power as yet unknown. In the real "Real World" machines may not have taken over, there might not even be machines at all. So in essence, if Zion is just another matrix, we, the audience, have no clue as to the real reason behind the matrices and the current status of the human race (if there is a human race).
I think that Derwood touched on this point very briefly, so credit goes to him where due.
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