They are in the process of building the Transbay Center [1] which would bring Caltrain closer to the heart of SOMA. Slated for completion in 2017. You can see the construction of it on google maps: http://goo.gl/maps/iMfZx
The TransBay development looks awesome. Reminds me a lot of Ogilvie in Chicago (exiting into the base of a skyscraper with integrated retail). It looks like the future--I'm sure San Franciscans hate it.