Re-reading the Architect transcript from Matrix Reloaded again (this should be made essential reading to anyone who's seen the film; they should make filmgoers sign a contract on entering the theatre.) Reinforcing thoughts in my head. This stuff was all obvious to me once, but too much information is coming from too many opinions being written as too much fact. Theories are blurring the truth - they are hiding the evidence in front of us.
When the previous iterations of The One have chosen (due to their "profound attachment to the rest of their species") the door to the right (that "leads to the source, and the salvation of Zion"), they were then "required to select from the matrix 23 individuals, 16 female, 7 male, to rebuild Zion". Simply put, the return of the One to the source caused the reloading of the matrix from scratch, but the One would also act to disconnect 23 people from the matrix as he knows it; they would be taken to the matrix simulation of Zion, also freshly rebooted. Back in the first film, Morpheus told Neo about the first person to be disconnected from the matrix, the one who released the first of the others from it. In the next reload of the matrix, in this sort of situation they would be referring to Neo. That is, they would if Neo hadn't potentially messed things up by causing "a cataclysmic system crash killing everyone connected to the matrix, which coupled with the extermination of Zion will ultimately result in the extinction of the entire human race". Bugger!
Why the existence of the doors, anyway? The doors may be there to allow Neo that essential factor of choice at the end of the cycle, during the end-game with the Architect when the artificial nature of Zion is revealed. (Choice: 99.9% of all minds would accept the program, as long as they were given a choice, even if they were only aware of the choice at a near unconscious level; that choice, if they could find it, facilitated by the possibility of finding their way into the real world - or the Zion program's simulation of it. People are always convinced there must be more to the world than what they can see.)
But that's getting away from the basics. As I said at the start, too much hypothesising just clouds the issue. I'll wait for the next film. (Or more likely, I'll complicate matters by googling transcripts from the Enter The Matrix game and the Animatrix shorts. Gah!)
But one last thought. Maybe schizophrenics are the true seers of the matrix. They can make sense of patterns in the algorithms of the code.