How about this? Neo is THE one, not just the one to free everyone from the Matrix, but THE one to actually put an end to the machines! So therefore, he has the power of to stop ALL machines, not just inside a computer program. I wouldn't consider it superpower, but who knows until nov. right? I mean we can sit and speculate all we want but we'll never know, until we see it right? Anyway, I don't think the machines went through the trouble of making a matrix within a matrix, they were probably pretty confident in the matrix keeping control over the humans, they didn't worry with it. But machines have a need for perfection, or a computerized version of it anyway, what the machine thinks is mathmatically perfect! That's not really a theory, but it seems too complicated to create a matrix within a matrix within a matrix within a matrix ... Oh, sorry.