Trains in Tokyo are usually packed during rush hour. If you are traveling off peak (as a tourist often would), you'll usually find lots of seats open. I've never had trouble getting a seat on he ring line or another JR line, simply because I was traveling in the afternoon.
GP lives and works in Japan so he doesn't have the luxury of avoiding peak hours.
Also, as much as great public transit is nice for visitors (I don't live or work in Japan, and being a visitor there is great), its primary concern should be its residents. (subway lines do get built using big migratory events like world fairs though)
Yes, but it isn't true that Tokyo trains usually don't have seats. If you work on a strict 8-5 schedule, then of course it usually won't have seats for you.
China on the other hand...