I had a friend who posited that the Wall-E/Inception scenario would have been a far more interesting prequel backstory for The Matrix than what was actually presented in Reloaded and Revolutions.

Basically, that the remaining "real world" humans were deluding themselves with this grand narrative of a lost war against the machines, when in fact it was humanity's own environmental screwups that blotted out the sky, and most people willingly submitted themselves to a simulated fantasy world that was set right before the collapse of civilization. And if there were multiple "one" persons or matrices or whatever, it was only to keep resetting the simulation and re-playing that golden period. Basically, you would turn the first movie on its head, where Morpheus becomes the character who has to question his world and assumptions, and break free from a tyranny of lies.