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With Northern California Unified Rail Service, of course. Also known as Prop 1A.
The Bay Area will continue sprawling out in all directions, but especially eastbound towards Stockton as the area between Livermore and Sacramento fills in. To the south Gilroy, Santa Cruz and Watsonville will become the new periphery and to the north it'll be Santa Rosa and Fairfield. Everything will be based around San Jose, as Oakland won't rebuild their train terminal (or at least not within a reasonable amount of time) while SF is increasingly a dead end compared to the opportunity in the Central Valley. ACE ridership will explode and surpass Caltrain, eventually leading to electrification somehow. Already ACE has enough political patronage to support Valley Rail (their Sacramento extension) and Valley Link (formerly ACEForeward), both of which will be leveraged when the time comes for a much larger upgrade. The Stockton Diamond removal is the first step in all this, as is getting San Joaquins onto HSR tracks south of Merced.
This has been coming for a decade, if not longer, and SF leaders have chosen to sit on their ass and not do anything about it. Since 2008 they could have built a Caltrain tube to Oakland and a Dumbarton bridge to alleviate congestion and housing issues, but this didn't happen and the former is mired in red tape and feet dragging.
