The Bay area is finally electrifying Caltrain, which has the potential to connect the South bay in more ways then the current commuter connection. BART is also being expanded both in the East bay and the South Bay. And the only reason you are not getting a high speed rail to South California is because politics got in the way. But this high speed train will go between Bakersfield and Merced, making it the first true high speed train in the USA. All this while the Metro in LA is expanding and adding much needed connections in South California.
This all said, Marin County is an incredibly affluent part of the Bay area, it could really easily fix their connectivity issues to the rest of the Bay area with better and more frequent buses (I wonder why they don’t).