The Doylist explanation is that of course the human brains are being used as computing substrates; the energy explanation is a symptom of how little the Zion people actually know about the world.
An alternative explanation is that the machines aren't using the humans for anything; they're just devoted to the most ethical treatment of these billions of people who believe themselves to be at war, and the only way to capture them and keep them sane is to hook them up to virtual reality and keep them complacent.
Every human is a prisoner of war, in the finest possible cell.
that's one opinion of a world driven by machine. But where machines are currently unable to feel compassion or show mercy, an energy optimization algorithm could easily be seen as sociopathic as it separates mother from child for efficiency reasons because an algorithm said it wound be a more optimal arrangement.
Specifically, IIRC, it was in test cuts of the film, and identified as baffling by test audiences.
I don't think anything substantive in the films is inconsistent with it (and the behavior of the agents throughout the films is suggestive of it), just the in-character exposition.
Which, to get really meta, you can explain as the filmmakers incorporating the inability of audiences to grasp, and projecting it into the film as an inability of the “free” humans to do so, so that (as part of the system of control it is established that Zion is) instead they were fed the “battery” story.
Yeah it's a shame because it was such a cool Philip K Dick-esque kind of plot point.
> Which, to get really meta, you can explain as the filmmakers incorporating the inability of audiences to grasp, and projecting it into the film as an inability of the “free” humans to do so, so that (as part of the system of control it is established that Zion is) instead they were fed the “battery” story.
Yeah and the original was already meta being a postmodern critique of society so it's a "yo dawg I heard you like meta..."
The live action films I don't think so, but a few of the shorts in the Animatrix were supposed to be an accurate history archive from the creation of the first machines all the way through the war and the creation of the Matrix. The shorts both included it and kind-of came up with an explanation:
During and before the war, the machines were mostly solar-powered, so blocking out the sky was a last-ditch effort by humans to stop the machines that almost worked. But the machines developed a new form of fusion that used human bio-electricity as some sort of activation or catalyst. They weren't being used as energy directly.
Which is weird because a spiritual predecessor (and another Keanu Reeves film), Johnny Mnemonic, uses a similar plot point where the brain is used as a data transfer medium.
Every human is a prisoner of war, in the finest possible cell.