In between Tokyo and Kyoto you have Nagoya Metropolitan Region, which has a population of 10 million.

There is no similar sized city in between the Bay Area and LA MSA.

This impacts the incentives to build in the US.

Metropolitan Areas in the Western United States are VERY far from each other. And this isn't because of sprawl.

Take a look at a satellite map of the Western US sometime.

The trip from Tokyo to Kyoto goes through several cities that have >200k people living in them, several of them being larger than Sacramento. Your point about Tokyo -> Kyoto doesn't change the previous issue of economics of trains due to lack of density.

Stops (and Population) on Tokaido Shinkansen between Tokyo and Kyoto: Yokohama: 3mm+ Odawara: 200k+ Hamamatsu: 700k+ Shizuoka: 600k+ Nagoya: 2mm+