The Caltrain station is used for mass transit, though. The idea for SF is to use the old transit building at Spear and Market since the Caltrain Station is already in use, though the TransBay terminal would be a logical alternative as it truly does connect rather pain-free to BART, MUNI, AC Transit, SAM Trans and Golden Gate.
Jack London Square is where the Amtrak station is, and would be logical, but in order to get into the City, people have to hop onto a bus and cross the Bridge to get to their final destination.
Or they can take BART, which goes into Jack London Square.