My husband commutes from Manteca to San Jose daily (Berryessa/101). Depending on the time of your commute, the Ace Train may provide you with a more relaxing way to travel. It can be costly so I recommend doing your homework first. http://www.acerail.com
Mountain House is a great community and, in my opinion, its market will bounce back much quicker than its sister cities within San Joaquin County.