They are both the largest population centers in California by any metric. This is not "decide in committee where people ought to go".
The particular station locations is much more complicated but still based on population centers but a whole host of NIMBY action pushed a lot of those into less favorable locations.
(Don't get me wrong. I love Shinkansen. That made my Japan trip so much more pleasant than anywhere else I have been. Not a single plane trip within the country. No need to pre-plan. Just buy a ticket and hop on. In California though, I know very few - they do exist - who regularly commute between LA -> SF. Regularly ~ a few times a month for a few days at a time)
It seems like the train should aim to replace a route served (poorly) by daily vehicular traffic.
In the Californian model, you decide in committee where people ought to go (which is everywhere represented by committee members) and design something too big and expensive to succeed.