ok this is my take on it....
99.9% that take the matrix as true are the real world matrix, the 0.01% that dont are in Zion, a extension of the matrix. I think their is no two matrices, Zion is in a small bubble of the matrix. They never left the matrix, as it would be very hard for one person (The first one) to survive after what happened to Neo at the start of the first matrix film.
The one is the factor that always the loop to continue, they give him the chose to end it all or do it all again. This way they get ride of their 0.01% that are trouble for the machines.
The question your ask yourself if you were a machine would you not factor a system in at the start to contain the rebels and cull them with less hassel ?
System with-in system.
You know what supports my Idea of areas in the matrix like Zion ?
The way the Ship operator wasn't able to track all the members through all areas of the matrix, so I recon that Zion is a 'cloaked' area of the matrix used to dump the 0.01% that dont accept the main area of the matrix. They need to empty it every often due to the increasing chance that Zion could affect the main matrix more due to Zions members freeing more people.
So they end Zion and restart the cycle aka the sentinal attack and the one rebuilding Zion from start.
I recon neo has control of this bubble area in the matrix ie the sentinals being disabled
Its like skimmin the fat of a bottle of full fat milk, you know its bad stuff so you carve it out ie destroy Zion.
Also, I recon Smith was only able to take over that crew member because they are moving from one area of the matrix to another
Also Smith can only affect the machines from inside of the matrix in the film if he can from the Zion it must mean they are still in the matrix. But you saw Neos powers expanding into new areas (Trinity reliving and far faster speed)
I recon its all just one matrix, but this difference in this One (Neo) is what changes all the factors, ie Neo can control the matrix bubble (Zion). If so Zion bubble could have a chance to live and continue.
I still want to know about this ONE AI that created the machines, WERE IS IT !
The big player is still in the back ground I recon.
I hope that makes some sense
I have missed something about Neos new found powers though.....
Its bugging me now
This is the point were you shout out like Austin Powers "Oh No ! Im gone all Cross eye'd !" ROFL