For cities that have, at least for the moment, stemmed or reversed decades of declining population, policymakers need to change the focus from "how can we make life better for commuters and encourage more visitors" to "oh, hey, let's make life nice for people who actually live here." BART's a system which was too much designed to bring commuters into the city, and doesn't function well as a "getting around the city" system. It'll probably take a miracle for the money to appear to improve its functioning in the urban core, but it is what they should be thinking about.
San Francisco, specifically, is at its historic peak population.