I just read a news story about someone suggesting that the High Speed Rail line in the Bay Area being run in San Francisco Bay, in pilings along the shore, so as to not get those nasty noisy trains near anyone. It includes gems like saying, "Why would there need to be a stop at SFO? Anyone who is at SFO and wants to go to Los Angeles would just fly there." Which of course misses the point that HSR is more than just about connecting the end points -- San Francisco and Los Angeles -- but is also about serving intermediate points with fast, frequent trains.
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.