Haven't seen Revolutions yet, but finding this explanation of the trilogy, and getting sent another one yesterday, reminded me of my own only-half-not-serious wacky interpretation. I quote from my email:

I'm still holding to my neo-Marxist reading of the first movie. The Matrix is a metaphor for capitalism, under which humans (the proletariat) are kept in a state of passive illusion (false consciousness) while the machines (the bourgeois) feed off their 'energy' (alienated labour). That's why the humans-as-batteries scenario is necessary, even though it's just silly in science-fiction terms - for the metaphor to work, the bad guys have to be stealing the labour of the good guys.

And then there's the scene where Morpheus tells Neo that most humans won't be able to leave the Matrix - that's basically Leninist vanguardism, where a small core of class-conscious workers (the Zionistas) get to do whatever they believe is justified for the revolution. Which incidentally is why no-one wastes any time worrying about the morality of shooting humans - all those security guards - inside the Matrix, when we already know that this will kill them in the real world: they're disposable because they're not part of the vanguard party, and therefore are working for the machines even though they don't know it.

And rearranging the letters of 'MATRIX' gives 'I.T. MARX'! It's all so obvious...

The real beauty of this theory is that it explains why the second and third movies are crap. The end of the first movie is the start of the revolution, which would be way too ugly and politically confronting for an American movie to depict. For instance: are the Zionistas really going to unplug all the humans, even though it would kill them? Surely a substantial number of the humans would agree with Cipher that ignorance and steak dinners are preferable to eating plankton in caves with a bunch of dirty commies, and would therefore form a Menshevik faction allied to the machines? And if the Bolsheviks win the ensuing civil war, do they get to have show trials and party purges? etc, etc.

As if.

Like I said, I'm only half not-serious about this. My biggest problem with the first movie was not the people-as-batteries nonsense, because it makes metaphorical and emotional sense; it's with the killing of innocent bystanders. The Zion guys are fighting on behalf of all humanity, so they must therefore also have some way of rationalising or justifying the security guards who get fragged in the famous lobby scene, the office workers who get a helicopter smashed into them, etc, etc. One of the cool things about the first movie was that it came as close to addressing this issue as any Hollywood film ever does.