Intuitively and practically, I agree that public transport is worse on in the Bay Area than it is along the Northeast Corridor, but qualifying and quantifying how it's actually different is a challenge. For one, the Bay Area's primary transit backbones are BART and Caltrain [1]; there is a missing link between East Bay and San Jose; there's not enough Transbay options; Oakland is the true hub of the system but not the primary activity center.

Also, most of the activity nodes of the Bay Area are actually close to transit, which paradoxically hurts the efficiently of the system. Traditionally, you'd want each station to be its own hub from a larger catchment area that you'd serve with, say, buses or other transit. But in the Bay Area, because of the Bay and mountains hemming in the built-up areas, every interesting node is already on the One True Circum-Bay String of Pearls, and have minimal catchment areas beyond them.

This also means there is no express option to get from one end to the other, without having to traverse through all intermediate points first, regardless whether that's accomplished with an 'express service' that skips stops, or a transversal direct line.

[1] https://upload.wikimedia.org/wikipedia/commons/0/0b/SF_Bay_R...