I think we have improved transport economics so much that the size of a metro area needs adjusting in our minds - London has commuters from Birmingham, Cambridge and beyond - in the same way that NYC has commuters from Pennsylvania and even Philly.
The winning City in an area sucks in all the surrounding populations - it's just now that transport links mean that those surrounding populations are in what used to be called other cities and are now just suburbs.
We need better town planning not ways to hold back cities to certain geographic locations
I propose, instead, that New York City is a suburb of Philly.
There are arguably more high end jobs in the suburbs surrounding these 3 major cities than in the city centers themselves. While this has removed the issue of one major city sucking in all of the surrounding resources, it has also distributed all of the problems of a major city center throughout an entire region - extremely high housing costs, horrendous traffic, etc.
Since each municipality in the Bay Area enjoys near ubiquitous power over local development and policy, it is also very difficult to implement effective regional plans to improve these issues.
I would be interested to know which cities are consolidating high density areas while growing such that they will have a Manhattan.
But I don't think every city needs Manhattan style density. Four, five story mid-rise density is the answer. Austin's urban core is building heavily in that style. I was just in Milwaukee for work as was surprised by the huge number of mid-rise buildings all over downtown. Just to show two midsized cities with insane growth at the core.