If you haven't actually been to Tokyo, you're talking out if you're ass. That's peak hours at the busiest stations in one of the most densely populated cities in the world. I've been to Tokyo and never experienced anything like that.
I live in D.C. and the metro system here is a complete clusterfuck with a tiny fraction of the riders.
It's the reality of all major european cities too. Paris has you smelling your neighbor's armpit for a good 15 minutes on crowded stations. Even my city of 400.000 gets crowded during rush hour and people get close together.
From what I can observe, I'm still alive, society hasn't collapsed or failed yet, and it's been this way for decades. A bit melodramatic aren't you?