How's $3600 a month in rent grab you? $500k for a down payment on a teardown? An added 30 minutes of commute time on a dingy BART train or averaging 6mph on the 101? Homeless camps and stale urine smells next to multi-millionnaire's homes and offices?
Finding, making, and keeping friends in the valley is double-difficult, because everyone's under such pressure to work extra hours, and the area isn't exactly renowned for its people skills.
If you're looking to settle down and raise a family, you might find the odds are pretty good in SV, though (in terms of single people in that age range that are family-minded and also worth marrying). At least until your kids need daycare.
As someone who's dipped a toe in both, I'd actually recommend giving further thought to the DOE deal. You might even be more fundable (and hirable!) after 15 years' DOE experience, moving to SV, than after 15 years' startup experience in SV.