I've said this before, but it bears repeating: On my trip to Japan, I took a train from the end of the Shinkansen line to the next stop along the line. A parallel regular rail track -- think the equivalent of Caltrain -- took around an hour to go between the two cities. The distance was roughly equivalent to San Francisco-San Jose. The Shinkansen did the trip in about fifteen minutes.
There aren't going to be a lot of San Francisco-Los Angeles non-stops. A sensible pattern of services like that in Japan combines super-express, limited, and lots-of-stop services. Major points would have all trains stopping there; lesser ones fewer trains. But all of the intermediate points would have some service.
I am really annoyed with the NIMBYs who are all in favor of transportation improvements, as long as it's somebody else who has to "suffer" for them.