Japanese passenger rail, by which assume you mean the slower trains and not shinkansen (because shinkansen is in another world of superior experience), is comfy as fuck and reasonably priced. As someone who rode Amtrak, you know neither of those are the case in the US.
It so fucking crowded its ridiculous. Im a dude and I still felt like I was getting molested.
It was crowded on Japanese intercity commuter rail? Was this a JR Line or a city metro line? Were you on peak hours?
I’ve been on hundreds of trains in Japan and the only time I remember it being too crowded to move are the ones early in the morning and the ones at rush hour.
They also get a little crowded in inner cities on Friday and Saturday nights, but you know what? They’re great. They’re almost never late, they’re comfortable, and they get you where you’re going. Cheap too. I remember going from Narita to Shinjuku (40 something miles) for around 2700 yen (like $24).
The best trains I’ve used ever are actually in China, unless the shinkansen in Japan counts. The shinkansen is the best transportation I’ve ever experienced. Surreal levels of comfort and smoothness.