There is a lot of development on the east side of Dublin, and that has a BART station as well, and a pretty direct drive to 680 as well, so those could be options for you too. But as I just told someone else, it really does benefit you to go to the new home developments with a realtor.
We truly can negotiate things for you (or at least I have....) that you cannot get on your own. The builders want us to feel confident referring people to them, so you can get upgrades, better financing, etc. by going there with an agent.
Also check out: http://www.arounddublinblog.com/2013/01/dublin-ca-holanda-la