Okay, here we go:
1: The whole war with the sentinels and the rebellion formed in Zion all takes place in a 2nd matrix. A matrix within a matrix, that is designed to subdue those who are resistent to the original matrix.
2: The 1st try at the original matrix was utopian and failed because no one would accept it. So it was re designed and now that is the current matrix that neo woke up from. Those who do not accept this matrix and wake up from it, wake to a whole new matrix that contains Zion and the war and that whole deal.
3:The 6 matrix’s that the architect speaks of are just re designs of the 2nd zion reject matrix if you will. There is always a “one” that is led to the core system by the system [the oracle is controlled by the machines in order to lead the one to the architect] Then the one makes a choice, either to save zion, or to save the ones he became close with in his matrix. IN EITHER CASE, THE ZION REJECT MATRIX IS DESTROYED AND REDESIGNED. Zion is then rebuilt with the “one” waking up new people to lead a new rebellion. (Morpheus speaks of this in the first movie about how there used to be a “one”. All the past “ones” chose to save Zion thus re designing the zion reject matrix to weed out the imperfections. Neo was the first one to choose to save the one he loved over the choice to save all humanity.
Because of all this and the 2nd zion reject matrix, neo now has powers that he never thought he had in his alleged “real world” [ZION MATRIX] This is a giveaway to this matrix’s existence. As a result of the use of this new power, he goes into a coma. SO does agent smith when he uses this new power in the 2nd matrix as a human.
Any problems you find with this, think about them before posting because i beleive with this hypothesis i can explain all the happenings of this film epic.