The only thing they have in common is that they're both near a fault line. Tokyo has a foundation of solid bedrock so soil liquefaction is not an issue. Very little of the area surrounding downtown Tokyo is sea, compared to San Francisco, which is a peninsula around 10 km wide.

Most of SF actually has quite shallow bedrock. As for the part that doesn't, it already has subways and tall buildings (except for the part near Ocean Beach). But anyway, we wouldn't actually need any tall buildings to solve the housing crisis; 4-to-6-story apartments would do the trick.

http://images.slideplayer.com/22/6340453/slides/slide_27.jpg

If being surrounded by water is an insurmountable problem, how do you explain the tall buildings and subways in Manhattan?

>If being surrounded by water is an insurmountable problem, how do you explain the tall buildings and subways in Manhattan?

I'm not saying the water inhibits construction. It just limits the area where you can expand. Look at New York on Google maps and zoom out a bit. The metropolitan area expands in all directions except the very south. Now look at Tokyo. It also expands in all directions except the south-east. Now look at San Fransisco. The north, west, and east are blocked by the Pacific Ocean. There are single long bridges to the north and Oakland, but they serve as choke points limiting movement. Much of the area to the north is also a national park.