Earlier quoted context omitted.
What the heck is the train line doing near Fresno? Why is it not following I-5 and making zero stops in between the South Bay and LA?
It's supposed to link the whole state, not just LA to the Bay
Put all the stations on sidings so that stopped trains do not block the main track. Trains operate point-to-point just like aircraft, with everybody getting on and off at the same time.
This means that there is little downside to adding more stops. The trip time for other stops is unaffected. There is no energy or time wasted on intermediate stops.