What a dishonest, cherry-picked example to justify your pessimism.

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).

Is it really cherry-picked? Or if it is, is it really that difficult to pick out the "cherries"?

https://en.wikipedia.org/wiki/Atherton_station

What do you mean? Redwood City is not that far away which has a proper Caltrain stop. And—just like Marin—Atherton in an incredibly affluent community.

Sure, I will admit, California has some problems when it comes to their public transit projects. But pointing to the richest communities and how they are not getting trains is not a good example of those problems.

EDIT: Previously wrongly stated that there was a BART station close by.

Caltrain runs once an hour for half of the day. You're screwed if you don't know exactly when you'll get to the station and find a parking spot.

Thats why I mentioned the electrification of Caltrain as a good public transit project in California. With electrification, it becomes far cheaper and easier to run the trains more frequently. Currently it is just commuter service making the South bay kind of disconnected from San Francisco for anybody but commuters. With electrification, this train has the potential to become much more then that.

I know it's quicker off the mark at peak times, but is the cost difference enough to run dramatically more trains?

Yes, electrified trains require far less crew and other workers, which means the current size staff size can operate on a wider timespan for practically the same cost.

Also the acceleration and deceleration will clear the tracks far easier and quicker for the next train to arrive, leaving less congestion during peak hours and less load on the system overall.

Well then something is broken with PT in your neck of the woods. Too bad for you.