The underground
is quite well develloped. But in the morning and afternoon, at peak-time, it's not fun to take it. Maybe you have already heard of the guys with white gloves pushing people in the underground to make sure everyone gets in. In the metro you can't move a centimeter, jammed between the sliding doors. Some kind of swing doors opening to the outside like the tram doors of Nantes wouldn't resist the pressure... When I get an occasion I will make a picture from the outside of a train for you, with people's faces pressed flat against the window. Be happy to live in Europe! In fact I profit of the fact that I need to take a line that's not one of the worst, and of the fact I'm 187: japanese are smaller than me, at least I got the head over theirs.
Evidently some men use this to grab girls asses or whatever. Personnally I can't imagine how to know if someone's grabbing you or if you're just jammed of all sides.
Hint for anyone coming to Tokyo: if you can reach the gangway, between the seats it is not that bad than between the doors.