You could go on forever about how it's a matrix within a matrix which is within another... And at each stage you'd get that 1% which refuses to believe it. The thing is that if they did use the plot that he's still within the matrix then why don't they just unplug him, kill him and dump the body? Would get rid of any rogue people pretty quickly and cleanly. Then again, I seem to remember there was some little bit of trivia that prevented them doing this in the first film... Bleh. I say just wait until they release the final part.
At least it's running NT. If it was 95 then it would only go for 47.5 days at a time...
- trevor