The Matrix inside the Matrix doesn't seem to be a very credible theory. BUt it could be and matrix revolution could answer all this questions that arrived after watching the first few instalments of the Matrix Saga. The Second Reconaissance (part 1 and 2) was meant to show us what the REAL world is and what happened to it and how the the matrix was derived. So if you accept the theory shown in The Second Reconaissance you believe that there is only 1 matrix and it's the architecture of the machines and NOT humans. But if you believe in the fact that there's a Matrix inside the Matrix, and humans were the architecture of this two matrix's, I have to wonder why this human architects will want to do something like that. Because I know for a fact if there was only 1 matrix, the machines created it so that the humans are placed in some sort of dreamworld while they were used as batteries. But if there were the human architects who build the 2 matrix's, what was his goal?? I guess only time will tell :D.
ANd, to add I kinda figured that there were 5 "The Ones" (as mentioned by the french guy at the restaurant) before Neo came around... See the architect at the end said the matrix was opened 6 times and Neo was probably the 6th "the one", it'll be time before the matrix was opened for the 7th time and Neo will be stripped off his post and thus the matrix saga continues almost endlessly.