Well, they are separate cities, since they have geographical boundaries and distinct city governments...

But yes, if the San Francisco Bay Area were merged into a single megacity with a unified, powerful municipal government, some of its persistent and increasingly painful issues (imbalance between commercial and residential real estate development, broken public transit system, etc.) might have a better chance of being solved.

Only in a legal sense are they different cities.

I mean you could legally declare that my legs and upper torso are different people, but it would be silly.

I realise there's history and San Francisco wasn't always joined to San Jose by unbroken urbanity, but arbitrary legal structures should keep up with geography.

I think if you looked at cities as density of buildings and people living/working as a set of gravity wells, then defining which direction things flow towards and from how far away would make where to draw the real lines less ambiguous.

In that respect places like New York, The (SF) Bay Area, Los Angeles, Atlanta, Chicago and Seattle would make a lot more sense; and most of these mostly would be within one state.

Problematically cities spanning state lines would be obvious. DC, Portland (Oregon), Kansas City and St. Louis spring to mind as examples.

I believe it to be unfair for workers to escape the taxes of a city by driving across some human chosen line.

I believe it to be unfair for insular communities to exclude "less desirables" by NIMBY actions.

I believe we could actually solve congestion if these mega-city regions had regional planning and zoning to encourage a range of affordable housing close to the jobs, addressing the commutes instead of trying to fund their expansion.

I appreciate the concept of the "Northeast Megalopolis" here on the East Coast, where we consider Boston to Washington DC one continuous city:

https://en.wikipedia.org/wiki/Northeast_megalopolis