Do you have any stats on apartments without baths? I know apartments with no showers exist but I haven't seen one since 2000. I don't know how common they still are. Prices of new apartments and houses are not that high (well, relative to NYC, SF). Sure there are expensive places like Meguro, but I see ads on the subways all the time for brand new 100m^2 apartments for ~$400k (I guess that's to your point that they are further out but don't a lot of people takes trains in to NYC from far away? I know Google offers buses from Walnut Creek to the Google Campus. That's 50 miles which I think is further than most of the reasonable prices places you can live in Tokyo)

Japan also has the interesting issue (like you mentioned) that buying a house or condo is not an investment which I find fascinating. It suggests to me not that housing prices always go up just because of "economics" but also partly by culture and belief. People in many places take it for granted that real estate prices go up so they go up. They expect them to go up. Japanese take for granted that real estate prices go down. To them buying a house or an apartment is like buying a car. After you buy it it's used car / used house and no one wants that (well, less people want that), they want new so price goes down on non-new stuff. If I understand correctly there are only a few small areas of Tokyo (Meguro being one) where prices of used apartments are going up. If you can buy the land, the land prices might go up but if you're buying an apartment/condo you're not buying the land.