The flaw in the US is centrally to do with suburbs and their existence: BART is for commuting into SF and little more. Basically each station is just another meaningless entry point to a larger mission.
In contrast, MRT systems (that work well) in most of the world (including HK and Taipei) are very different — they seek transport between any corner of the city/region because every station has “destination value” for a significant part of the ridership: “every station is a destination and has its own indepenent raison d’être (reason for existence) rather than merely being subordinated to one terminus (SF for BART).
The pervasiveness of this monomania is the problem with BART and it’s reinforced by zoning and separation of function: suburbs are for sleeping, urban centers are for working and malls are for everything else (compare to US 40-50 years, and yes, this is reality only now being usurped by the internet itself). These is NOT the situation in most other cities of the world and MRT environments where both human modes are together cheek-and-jowl, which both makes the city and the MRT system work.
The other fact is population density which is thwarted by suburbs quite obviously but is also thwarted is “cities” like SJ and SF which by population density alone are not actually real cities at all.
I’ve had the pleasure of living in Taipei and the contrast is stunning: Taipei works while the SF Bay Area is utterly broken and unlivable. Mass transit is part of the issue but the entire vision and reality of urban planning is also deeply flawed and failed.