Somehow im lead to belive that the one or the anomaly is a program to keep the rest of the human race in check becuse for some odd reason, the same things happen over again and Zion remains to be called Zion.
Because Zion is another form of control. It\'s called Zion each time because the humans who continue to choose the reality of Zion over the reality of 1999 need a place to be shunted until the anomaly of the one can be solved in which case all humans would choose 1999 and there would be no need for Zion any longer. Once the one emerges from the Matrix, the machines do everything in their program to lead him to the source and restart the system so the machines can try to solve this anomaly once and for all. Each time, as I said, the machines have to change certain variables to come closer to attaining this goal. One such variable is Trinity and the rest I explained in my post above.
Once the Matrix restarts when the one merges with the source, any memories of Zion are purged since all those who do remember it are subseqently killed when the machines enter Zion and kill everyone there as they have five times before. If there is no one who remembers, then the information can\'t be passed on to anyone.
If programs can hide from the matrix and somehow detach themselves from the machine mainframe then its just as possible for neo to be a walking program that resets its self.
This I can see happening, but I\'m not sure I agree with it. For the most part, machines only decide whether they live or die when they face deletion. For example, all the rogue programs in the Matrix mentioned during the Oracle conversation as well as the Merovingian\'s guards (the Twins and others) are programs who chose against deletion to live inside the Matrix. That\'s the only example of free will I can think of. Neo has been making choices all this time, but I must admit, his continuance to follow orders and behave just as he is told mimics that of a machine more and more.
To contrast this, Smith himself is beginning to act more human despite the obvious presence inside a human body. It\'s interesting to be sure, but these two apparent foes could possible become allies seeking the same goal in the third movie.