It is not a very good argument to call SF seismically active and then compare it to Tokyo. Tokyo sits where three active fault lines converge. Having lived in each for a year, you can expect to experience more activity in two weeks in Tokyo than a year in SF.

Also, claiming that most of Tokyos subway is above ground is incorrect. The subways, Tokyo metro and Toei, are nearly entirely underground within the city center. This is hundreds of stations. Yamanote line is part of an entirely different set of trains for longer distance transit.