If the ABAG had power, I would have them replace Caltrain with BaRT to make a it a loop around the SF/SP Bay Area and tear out CalTrain. Caltrain remains because the tracks are used by UP --if it were not UP's right-of-way, BaRT could have that corridor. BaRT could still work if they did cut-and-cover to build a parallel line under the Camino Real. Granted that'd be a lot of money today --they should have bought in back in the 60s. I know, hindsight and all.

The main issue then would be what to do about Gilroy --they can keep Caltrain for that like the ACE does for the East SF Bay.