Agreed. 196 cm/6'5" here, and the only thing I found lacking was the width of the chairs on the Tokaido line (3+2 arrangement). I'm not sure what the pitch of the seats is, but I had plenty of leg room (much more than any train in the Netherlands anyway, let alone air planes).

If you ever find yourself in Japan with a rail pass, do use the free reservation option when traveling between Osaka and Kagoshima with the Sakura. That one has a 2+2 arrangement in the reserved seat cars, which makes for a more comfortable ride.

I do agree with things being quite small/low though, bumping my head at least a couple times a week.