Party Boat posted:

In the MMO (which was canon, apparently) it was eventually revealed that Neo and Trinity both originated from research into humans and machine code directly interfacing (i.e. without using the matrix). Most of the third film is spent beating you over the head with the idea that there's no real difference between a human mind and a simulated one, so someone being "resurrected" from the matrix certainly isn't out of the question.

I would also be down for the Wachowskis ignoring as much of the previous canon as they want.