At one time the HSR was supposed to go down I-5. That makes sense if the ONLY service you intend to provide is SF-LA. However, as a transportation system that makes no sense because there are significant midpoint traffic generators to consider, and it would just activate the airlines to kill it (who do you think killed Dallas-Houston-Austin HSR some years ago in Texas? Southwest perhaps?). As a useful piece of the transportation system, the Japanese approach - a moderate number of intermediate stations with express bypass tracks and connections to good local and regional transportation - makes more sense.

I do agree that political reality is producing more stations than the line should have. I see no reason, for instance, why there should be a stop in Hanford. The original idea that seems to have slid under the table was to keep the current Amtrak service with track upgrades to allow 90-100 mph in the Valley, to distribute traffic between the smaller towns from the HSR stations (Fresno, Bakersfield, and Los Banos or Merced at that time). THAT makes sense; HSR stations should be at least 100 miles apart. But remember, politics is the art of the possible, and you often have to do things that aren't exactly what you want in order to accomplish the bigger project. And as I noted in another comment, expresses don't have to stop at every station (see: Acela vs. Corridor trains on the East Coast).