Protoclown and Sarcastro: That's a very interesting point. The only question I'd have would be, haven't the machines already significantly surpassed the initial programming that the humans are responsible for? It would seem a little strange - although completely possible - that they will obey this
prime directive, but ignore everything else that would most certainly be an inherent part of their programming (i.e. protect humans, never harm them, etc.). Ofcourse this does not negate the point - somewhere deep down in their BIOS (heh) could be that single command that they must obey.
My point before was that, if this is the case, the 'matrix' seems inefficient. The same energy could be extracted from comatose, or at very least, constant-REM-induced humans leaving zero room for rebellion (no communication, etc.). Unless somebody mastered lucid dreaming and became the "One" in that sense and oh I see a parallel
Like I said, I don't claim to understand much about this (I've only seen each one once and both times I was not exactly in the state of mind to remember details) - so if I missed something obvious, my apologies.