It was simple. I know how some people didn't get it, and I'm very sorry for you, and if the first movie was too much for you to grasp, then lolwut?
Anyhow: the Matrix was simple to a fault. Any human could escape.
The problem for the machines however is that the world could reset. Yeah, that was a more of a mindf**k than n°1.
But when I saw the Matrix Reloaded, my first thought wasn't: "Hmm, Neo has special powers now. That must mean he's Jesus."
"Hey, what if the world resets :D"
No, my first thought was:
"HAH! The machines were smarter than all of you combined! Did you really think they'd have just one matrix?"
You see, Neo was using powers, Smith could "cross over" and the world could reset, it had happened before, and yet the Wachowski's refused to embrace the idea that there might be another matrix within the matrix. Why not?
If you've seen inception, you see how confusing it can be. And that's exactly what the machines want: you want people running around inside your programs until they die of old age, nice little batteries as they are.
So, I created a much more effective model. If the world ever gets taken over by machines, this is how they should do it. I apologize in advance if this happens for real, because it's not a very nice model.
I know, I know, no funny pictures. Not feeling like a funny picture (not to say I'm unhappeh or anything). The old blog might come back, it might not. But weirdness and nonsense will never die!
And come on, how much more nerdy can you get than coming up with a better matrix? (aside from actually trying to programming it in kernel :p)
That's it. :-)