Electrified Caltrain is infinitely preferable to BART.
[1]http://www.caltrain.com/projectsplans/CaltrainModernization/... [2] http://www.caltrain.com/Assets/Caltrain+Modernization+Progra...
What would be the advantage of BART over electrified, grade-separated Caltrain? I'm hard-pressed to think of one, and there's definitely one major disadvantage: the nonstandard rail gauge.