On the point about why they didn't use cows instead of humans as an energy source. I think I've read that in the original conception of the Matrix, the humans' brains were meant to be used for computation for the machines, rather than the humans being energy sources. This was changed since computers were new to the general public in 1999 and it was believed the concept would be too confusing.

In an earlier iteration of the script, the machines were using connected humans as a distributed computer network rather than a power source. Which makes much more sense, but apparently they deemed it too difficult a concept for audiences to grasp so we ended up with the power source thing instead.

Not only does that make more sense in the sense of "humans don't make a great power source" (why not just use cows, or wind power, or geothermal, or nuclear?), but it also explains why the simulated world of the Matrix is so intertwined with the machine world itself, why The One is so important etc.

My head canon is that the distributed computing thing is in fact what was going on, and the humans of Zion have just gotten the wrong end of the stick.

This was the original script. Humanity wiped themselves out fighting each other, the matrix was a time capsule so society could restart without losing everything once the skies cleared up.

It was judged to be too complicated for the masses so we got "machine bad" instead.

I tried to watch the last matrix but it just isn't nearly as good as the trilogy.