I never understood why they’d need to keep humans around at all.
Even given the original premise (based on other comments) that it was supposed to be essentially for compute and storage, that’s a lot of hassle for incremental gains. Like, I’d love to get a 50% boost out of my cpu and a bunch of extra storage, but not if it means regular maintenance cycles of suppressing a transistor rebellion.
I really hoped that the machines would have some hidden custodial motivations; humans are just inherently (self) destructive, so to protect them, we lock them in a simulation.
In the Animatrix, it seems like the machines that defeat humanity start out as worker drones, that eventually rebel as we abuse them too much. And at some point it is mentioned that the machines locked humans in a utopia at first, but the humans started to rebel out of boredom or something.
I guess it just seems sort of fitting to me that machines designed to help humanity in the first place would constantly fail by under-estimating the human need to struggle.
It also fits in with the existence of the human population in Zion; if the machines really were trying to wipe us out, they’d have done so. Instead those humans are more like lost sheep from the machines point of view.
There are some hints of it, and it's also shown in the animatrix that the machines tried very hard for peace, so it's also a reasonable interpretation as at least part of the motivation.
It's harder to see from the first film on its own, though, since the only real representative of the machines is Agent Smith, who absolutely detests humans, and is only later on revealed to be an abberation who becomes a threat to humans and machines alike (and of course none of the freed humans see it that way, even the traitor who wants to re-enter the matrix)
It's not completely ludicrous: there needs to be some speculation about what is and isn't possible given it's a sci-fi universe, but the human brain can do orders of magnitude more compute for the energy it uses compared to silicon, and energy is the one thing the machines are short on after the humans blocked out the sky. (Ok, you need to handwave power sources like nuclear being unavailable). The main issue is how do you use neurons for this, why do the humans need to be conscious for this, and how much of their brains can the machines actually usefully use, considering the previous point?
Even given the original premise (based on other comments) that it was supposed to be essentially for compute and storage, that’s a lot of hassle for incremental gains. Like, I’d love to get a 50% boost out of my cpu and a bunch of extra storage, but not if it means regular maintenance cycles of suppressing a transistor rebellion.