Technology

There was a youtube video I saw about this recently that suggested that it was never actually humans that blotted out the sky, it was actually the machines that did that, since most life on Earth depends on sunlight (directly or indirectly), humans were hurt more by the sub-blotting than the machines ever would've been. Plus, there's a reference in the script for one of the movies that talks about the clouds in the sky being some sort of nano-machine clouds or something similar.

Zion has been destroyed multiple times and rebuilt by the machines themselves, so any history that the Zion humans have is what the machines want them to know and has likely been tainted. They also point out that Zion uses geothermal energy for its power needs, there's really no reason why the machines couldn't also harness this power (and since they're the ones rebuilding Zion, they would obviously already have this technology). I've heard that if the machines really wanted a living power source, they'd have been better off using cows and just make the Matrix simulate green pastures, rather than waste all the time taking care of humans.

I've not actually seen the last Matrix movie, so no idea if this was brought up/contradicted in that, but seemed like an interesting idea.