Matrix Three -- a rambling on what might have been. . .
This is a speculation posted months before the final chapter of Matrix came out. Lots of theories, but this is my interpretation of things and how they should have worked toward a resolution.

Well, it all seems to be stuck in some kind of infinite loop. Perhaps Zion is a program that is used to generate the energy needed to power everything and the Matrix we currently know of is a decoy (or a sub-program to deal with certain given personality types). By giving humans a bogus cause to fight for -- an enemy to defeat -- it does two things:

1. keeps them from actively fighting the actual menace
2. Provides additional energy

That would explain Matrix related prophesies (when is the last time you met a truly rational person who bought into prophesies). It would make sense to plant some kind of hope like that to distract humans.

Of course it could be VR's within VR's within VR's.

If Smith is a virus (or a machine bound to a virus) and Neo is a human bound to a program, then clearly there is a third party. Also, it is likely that others could have less active (or obvious) bonds to programs. Morpheus for example could have been bound to a routine that pushes him toward finding and helping the one. He is somewhat monomaniacal in his beliefs about the the prophesies and risks everything to accomplish this.

If we accept that there are programs -- then there is a certain amount of pre-determination in the world (Programs designed for specific outcome -- like an assembly line robot). Two plus two will always equal four unless programed to equal 5 (or programed incorrectly or designed to give an answer based on some variable rather than a constant). Whatever the final answer is, it won't change unless the variables of the given programs and the routines that handle them are designed without constraints. However, if the program is designed to be self-correcting (that is, it compensates for variables that are out of bounds and answers outside a certain range of parameters) then it will always get the desired end.

This leaves us with two basic possibilites:

1.) The programs governing the world(s) either have a set outcome or an unexpected outcome. (That is it knows how things will end or it doesn't and is designed to output whatever comes of it).

2.) There is an error in the programing that will in effect either reset or stop the program if something occurs outside of its given parameters.

If we accept that the primary function of the program is to keep the humans subdued and producing energy, then it follows that the program is designed to reset to that end, regardless of variables or outcomes. i.e. when all is said and done, the program reboots and the whole affair starts over -- either with the initial set of constants and variables, or it mutates based on input from the last iteration. So, it reaches it's conclusion, and then filters the final set of variables, reassigning them either new or pre-set values then resets constants based on outcome of some "standard" set of values. If it also compensates by altering the running of the program, it can base it on outcome or random variables: available_cities = city_array[LA, Chicago, New York, Paris, London, Orlando, Moscow]; Neo_Lives_in = neo_city[city_array[random_city]; and so on.

In effect, everything is probably being done to distract both the machines and the humans, and is designed to manipulate them in a war among themselves, to keep them from their true function -- which we actually shouldn't have a clue. This would force the whole ending to be a Deus ex Mechina in which the the likely outcome will be a Mechina ex Deus.