I'm guessing that there have been multiple constructs of the matrix (more than 6) but only one Zion. I think this part is a lie. Or, the idea of Zion in the matrix has been destroyed multiple times, thus repressing the thought by those entrapped trying to escape.

I think the machines need Zion. As said in the first movie and this one, the first Matrix failed because it was too perfect and humans didn't know how to handle it. There probably wasn't a One in this world. The Matrix builds that worked better kept 95% of the humans in check. Good numbers. As long as they could fight the other 5% and keep them down to manageable numbers, things kept on moving. But when it got to be too much, when the One showed up, a new Matrix was needed. Those in Zion are getting stronger and the machines realize this and have to do more than just keep things in check.

The Architect is giving Neo two choices (choice matters), hoping he'll take one but being OK if he takes the other because of his confidence in ultimately succeeding.

I don't think the architect is human. He is the MCP and Neo and Morpheus are Tron and Flynn.

Fer"MCP=Matty Cow-Patty"rick