Bay Area has regional government, such as it is, in the form of MTC, Metropolitan Transportation Commission, & ABAG, Association of Bay Area Governments. MTC is a designated metropolitan planning organization (MPO) by the federal government, ABAG is the area’s recognized council of governments (COG). MTC appears to be in some senses absorbing ABAG planning roles now.
It seems that envisioning future Bay Area regional government should include examining what MTC / ABAG do now, how they were created and have been run, and how they are evolving or might evolve. Particularly, how they might evolve or be supplanted by forseeably viable legislative action at state level which might grant them greater powers.