CalTrain now faces an even worse crisis and weekend service is on the chopping block again.
What the railway really needs is new, dedicated source of funding, but in the meantime, I'm going to re-post one of my suggestions for cutting the cost of weekend service.
Let's take a look at the current weekend schedule. Trains depart from both ends, on the hour, making all stops, taking 96 mins to make the whole run. Obviously, an hour into that run, two more trains are departing from their respective termini--so there's a total of four trains on the line for most of the day.
The number of simultaneous trains, and their crews, are the key to CalTrain's costs. One way to reduce this would be to simply halve the current service, and operate trains every two hours, so only two trains and crews are needed.
But here's another, IMHO slightly better way of doing it: prune away stops to a "semi bullet" schedule, stopping well-spaced stations (maybe: SF, MB, MS, RWC, PA, MV, SC, SJ), a run that can be made in about 1:15. Run trains at 90 minute intervals. The schedule can be covered by two trains and two crews.
A 90 minute spacing between trains is better than two hours, and for passengers making longer trips (between stations still served, obviously), speed would be improved.