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*****SPOILERS (as if you're still reading)*****
I don't think Zion has to be a second matrix for the story to work, though that is an appropriately brain-warping idea.
Zion is a pressure-valve for the building inconsistencies in the programming of The Matrix. That 1% that don't accept the program escape and build until there's a community in Zion, and eventually, along comes The (well... A) One, whose job is to zero out the accumulated inconsistencies and reset Zion to its starting point. It's been 100 years since the sixth Zion reset. The myth of The One as a savior was planted in each new batch of Zion settlers in order to have them continue collecting those who don't accept the program. Morpheus turns out to be just another Machine dupe.
I'm also puzzled about the choice thing. Why should The One be given any choice in the matter at all? Why does the architect offer two doors? Except to allow the Brothers to explore a "love is the choice" theme? Thoughts on that?
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