The Matrix has one huge plot hole: There is nothing sacred or special about the way humans extract energy from food. You can do the ATP cycle in a vat and get the same results but you never break even or get a net energy gain. If a post-singularity AI needed to assure a continuous energy supply, that has to be among the worst possible ways to do it.
The explanation given in the 1st movie is quite the interpretation of the humans and far from the truth. In the 3rd movie the Architect explains why the humans are bred and why Zion exists.
I'm not sure I'd call it a plot hole but it's a pretty weak explanation. Something like using humans for processing capacity or something like that would have made more sense at least in a handwavy SF context.
> Something like using humans for processing capacity or something like that would have made more sense at least in a handwavy SF context.
ISTR reading that that’s the original explanation, and it is what the depiction of the programs-as-people (and agents specifically actively replacing people) is grounded in. The exposition—but just the exposition—was changed at studio direction based on test audience feedback.
(Personally, I think the change to in-character exposition is an improvement, not because it is plausible, but because it foreshadows and underlines that the “free” humans understanding of the Matrix is ultimately grounded in deception intended, as later made explicit, a system of control.)
Of course, I don't accept the reality in which the sequels exist :-) I admit I was pretty much in the school that The Matrix was a cool film and didn't really dive into the sequels and what they meant too deeply.
