I'm grateful that we decided to do this in a way that has fewer negative externalities, and probably lower total cost to society, than a freeway expansion. Seriously, we're lucky that the intention behind BART gave us anything resembling a train.

If you try to read it as a way to connect urban neighborhoods (like Manhattan's subways), you're going to be disappointed, because it isn't one.

Remember that most city land area is essentially suburban, and that SF/Oakland/SJ are less than a third of the region's population. Transportation that serves the needs and preferences of the regional electorate is vanishingly unlikely to resemble the Manhattan subway system, or make any sense for the tiny minority of us living on urban blocks. It's going to look like BART and Caltrain: infrequent stations in low-rise neighborhoods with big parking lots, infrequent service outside peak commute hours, etc.