Back in the day, SP only ran Coast line trains (Coast Daylight, Lark, Starlight, Del Monte, Coaster, etc) and the commutes into San Francisco. Everything else ran from the Oakland Mole with SP ferry connections to the Ferry Building until 1958. At that time you could actually consider the Ferry Building San Francisco's primary railroad station. After 1958 and termination of connecting ferry service, they ran buses over the Bay Bridge to the 3rd and Townsend station.
Just before Amtrak, the predecessor trains to the Coast Starlight were the Coast Daylight and the Casacade. The Coast Daylight ran into San Francisco, the Cascade ran out of Oakland. If you wanted to connect from Southern California to the Cascade, I think you had to take the San Joaquin Daylight and connect at Martinez, not the Coast Daylight.
They changed to Oakland and dropped San Francisco because Amtrak connected the two trains and ran through (at first only 3 days a week), and that was impossible through San Francisco. Other than that, the current system of bus connections is much like what SP did before Amtrak.
There never has been direct rail passenger rail service from San Francisco directly to the east, either before Amtrak or after it. SP did consider providing direct passenger service over the Dumbarton bridge and Altamont Pass, but they never did it. It just took too much time over the ferries.