Most of the benefits of bringing BART down the peninsula could be achieved by grade separating and electrifying Caltrain. What's more it could be done at a fraction of the cost and you'd end up with a better, faster system than BART.
<sarcasm>
But why would you replace the huge, powerful Diesel engines that blow large billowing clouds of exhaust fumes with wimpy electric trains? And would we still have the crazy searchlights and blaring horns that scare the cattle off the tracks in the middle of the night?
</sarcasm>