The 2nd layer of the matrix would be a viable assumption if the only reasoning behind the theory was the constant use of the word "backup" in the last 15 minutes of the movie. At the end, I think the building was a symbol for the entire virtual existence, powered by two systems, both which must be taken out to truly succeed.
Either that or Neo went on this entire journey in hopes of finding exactly what those 11 herbs and spices are. How else would you account for Colonel Sanders sitting in that chair at the end?
