I don't get this thread... both cities are close enough in salary and cost that the exact economics become less of an issue. Other things, like the cities themselves and the people in them become more important.
I completely agree that there is way more to life than economics, but for the young single engineer the business case for Bay Area (and even more Seattle) is very compelling.
To put it in perspective, when I compare myself to a friend with similar skills my net worth is already 2x greater.
Some people choose to make less to lead a different lifestyle, and would happily give up that 2x net worth to do so.