there is something else to potentially take into account: the matrix online game they're working on. According to the few snippets of info on it takes place after the Matrix:Revs and with an intact matrix.
(also remember that morpheus said that most people just aren't ready to leave the matrix)
what if man indeed defeats machine but chooses not to destroy the matrix? instead leaving most of it intact, with it's programming (i.e. agents, etc) but with under overall human control? Or even under an 'alliance' between man and machine (taking into account that counsil-dude what's-his-name said that man can't go without machine but that machine likewise can't go without man?
Of course it's also possible they **** up the ending completely thus creating a George Lucas New Star Wars Style Turd of Trilogy.
In the Matrix anything is possible!
