Everyone's public transport system looks shabby compared to Tokyo.
There's nothing in the world to complain about aside from that.
Because you are closer to paying the real price of the ticket than in Paris where transportation is heavily subsidized by the state. In Japan most train companies have now become fully private.
Meanwhile here my nearest Caltrain station has some car repair places and a mystery fondue restaurant that never seems to open. I think it's a money laundering scheme.
Well look at Paris' metro and its lack of elevators and escalators. Most stations have none! Good luck if you are in your seventies and your legs don't carry you anymore...