Looking at current train tickets for this route, the train to train transfer is in Bakersfield and from Emeryville to S.F. it is bus.
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I think the bus-train-train-bus-train route is the fastest one.
There is an Amtrak going the whole way, but is is so slow, that the transfers actually speed the travel up!
For some reason, it is the slowest of Amtrak scheduled trains, goin like 15 mi/h.
If they would be able to speed up the train, this may work.
But I would say, the train speed is probably caused by track issues, which would be beyond control of anybody.
Most track speed issues are due to the Federal Railroad Administration and their regulation mandates with respect to passenger trains. Most of these are due to signaling mandates, e.g. faster than 79 mph top speed (centralized train control and Class 4 track) would require adding cab signaling, automatic train stop and an increase in track classes that requires more stringent accuracy in track gauge, heavier rails (115 lbs per yard or greater), concrete ties, etc.
For example, the northeast corridor (former Pennsylvania RR) under Amtrak’s ownership has 140 lb/yard rails. Believe it or not, a lot of new “light rail” tracks have 115 lb/yd rails, even when they aren’t required to share with freight trains.