Exactly. At the very least it should be between Sacramento and San Francisco. A few people I know do 2 hour commutes living in and around Tracy/Sacramento area because it's the only way they can afford to own a house. But then there's no real jobs there and they have to come to SF for that. There's no solution in sight for the "larger" bay area.

(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)