This is just a theory, but the MetaCortex product seems to be some sort of videogame system that simulates reality. I know it's kinda obvious and a bit cheesey, but isn't it odd that Neo was working for a company that essentially is trying to emulate reality, as the machines are doing for Neo? To take it a step further, since the machines are not human and obviously could not have completely understood humans by themselves, could they have used the human programming taking place in the matrix to aid their simulated reality.
I mean, if a person in the matrix is trying to build an AI, can't the machines steal that code and incorporate it into the matrix code? As the Architect said, it took the machines a while to get it right, but did they do it all alone, or did people like Neo help them?
Ponder that...
: )