I think that Zion is real, but controled and known to the machines. The conselor and Neo discussion about not knowing how the systems worked in Zion. I think they let the free escape to Zion, Create the one, and basically keep the war going, to keep eyes from somewhere esle. The machines have known the outcome 6 times now, because they no how it starts. The kicker is the comment of the The architect to Neo that he is different than his predescessors, which means to me he has the albility to something the others could not.
im not really sure what you mean
Neo
I'm interested to know who the predecessors to Neo were?
I would imagine one of them would have been the biblical Noah.
He was allowed to take so many humans with him.
Actually, the theory is that everything is controlled by the matrix, even Zion. Matrix creates zion, according to the architect, and the matrix controls zion's population, extinction and rebirth. The oracle is only a machine that guides Neo in the direction it was programmed to. Neo doesn't want history to repeat itself, therefore he chooses to save Trinity instead of "saving Zion". By doing this he brakes the cycle of the matrix, and now they actually have to fight for Zion.
zion may be one of the results of the matrix but it was definitely not created by the matrix or the architect for that matter. Zion was a human creation that the machines have used as leverage because it too is dependent upon machines for its existence.