Danny Chai***** Matrix Revolutions Spoilers, kinda *****
You know, it’s been asked why the machines didn’t just nuke Zion. But I think it makes sense that they didn’t. Just, the m.o. had always been that the previous One populated a new Zion, so it needs to be habitable – you nuke it and that’s no longer possible.
Still not sure why they just don’t have tons of EMPs everywhere, though. Unless EMPs take out other EMPs, which is possible. That would explain why they’re only on ships, because the ships tend to be off on their own.