There have been many proposals to combine transit agencies, some with merit and some without. I am not going to join that argument here. The thing that *is* needed is a rational fare system so that a degree in fareology is not required to determine the cost of a trip.
I am far from the first to bring up this topic. Here are lists of transit organizations in the Bay Area - definitions vary.
https://www.seamlessbayarea.org/blog/transitagencieslist
And then we have (for example) a proposal:
https://www.seamlessbayarea.org/integrated-fare-vision
I don't know what would be the best way to rationalize the Bay Area (or beyond) fare system, zones (as here) or km traveled (as in The Netherlands) but both work. In German this is known as a Verkehrsverbund. For detailed information one must use the German Wikipedia. This is a computer translation of that site. Not bad translation, but keep it that in mind.
https://translate.google.com/translate?hl=en&sl=de&u=https://de.wikipedia.org/wiki/Verkehrsverbund&prev=search&pto=aue