They are connecting the BART right now. The high speed rail was supposed to be for commuting not alternative to airport (though there would be less groping involved I think making it viable for those who the airport degredation). High speed rail could be viable to compete with airports too especially if you're not in one of the two cities. The high speed rail is more than just two points. I know the yuppies and hipsters hate everyone who doesn't live in the two cities, but California is bigger than those two dots on a map. We already have people commuting to the bay area cities and towns from the central valley.
Rail is very viable in Europe and Japan for instance and are commonly used. More luggage space, larger seats, don't need to arrive a couple hours before departure, stations are closer to where you want to eventually get to, and connect directly with other mass transit. America really is very far behind in mass transit overall. The cost is high to build but if we used that excuse we'd never have an interstate system, or airports.
Best way to reduce congestion or overcrowding of cities is to let people be able to live outside of the cities. You don't solve that with airports or local mass transit.