Sheesh, yeah. SamTrans 397 takes 2.5 hours (a whopping 14 MPH) just to get between the city and Palo Alto, so missing that last train at midnight really blows. And one night I learned the hard way that neither Caltrain nor SamTrans run past 9~10 PM (!) on Sundays, so I had to take a shuttle from SFO.
I guess the OP has the MVP right there: start lean with one-two shuttles after midnight and if it works, expand gradually.
Having a night-only bus narrows it down sufficiently and I think you can even find interesting marketing twists which can apply for the benefit and fun of both you and your night owls (err... customers).