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Suggestion #2 is probably feasible outside of the core commute hours -- which is inline with constraints because Caltrain runs trains more frequently during commute hours already (ie. this service is not needed then).

I've done 101 from SF to SJ in about 40 minutes at midnight. Multiply that by 3 for rush hour.

Ok so they've already really factored in all the time for all the stops and the inevitable delays... Wow, then my question is... why is the train so slow!

The train makes many more stops.

there are three level of trains. baby bullets go from san jose to sf in about an hour with very limited stops. there's local express which have more stops than baby bullet, but don't stop at every station (gross oversimplification). And then there's the trains that stop. at. every. single. s.t.a.t.i.o.n.

I live in San Mateo, makes it super easy to split the difference. ;-)

Driving takes <1 hour without traffic. Could take >2 hours at peak commute hours.