I find it difficult to believe that there would be a matrix within a matrix. The reason why is because then who truly are the enemies (bad guys) and the saviors (good guys). Without knowing the good and bad guys doesn't that make for a rather lame story. Anyways, tell me what you think.
sorry dude, but i already started a thread with this exact topic. you're a little late to catch on to this kind of stuff.
Matrix in a Matrix (http://www.matrixreloaded.com/showthread.php?threadid=847)
http://www.matrixreloaded.com/showthread.php?s=&postid=6748#post6748
This is a "Mainframe attempts to create a perfect ecosystem" theory. If you can't accept the matrix and be a good little "copper-top", then we have another matrix for the "free thinkers".
The theory could explain a good bit but it is out there.
Not much more out there than the story that humans are harvested for their energy, no? :D
-WC-