Bus systems are on the city or county level

Slight nitpick: San Francisco is a consolidated city-county, so saying that bus systems are on the city level is slightly misleading (although the situation is still overly fractured). I don't think there are any counties with separate bus systems within the county, and as far as I can tell the different systems try to have at least some connections (VTA buses stop at some Caltrain stations, etc.) So as long as everything you're going to (e.g. Silicon Valley) is within one county, it's not too bad.