Palo Alto isn't a lot cheaper that San Francisco it has a reputation as being much more family friendly and has some good schools. Also, Mountain View, Los Altos, Sunny Vale, Santa Clara are all more affordable and family friendly than San Francisco.
Disclaimer: I'm a single guy with no kids, so what would I know?
The cost of living is another matter. A very basic starter home will in Palo Alto will run $1-2 million. Not unattainable for an engineer, but it will require some sacrifices.
$5,000 * 12 / 0.28 = ~ $214,000/yr salary
I could see that for a very, very senior and specialized engineer working at one of a handful of companies, but that's probably double the norm in the 'Valley for your average 5-10 year experienced engineer.
Not to mention having to have $200,000 in cash for a down payment sitting around. Even if you saved as much as $1,000 a month, it would take you over 16 years to build up such a down payment--for a STARTER home!
Key insight: old people vote.
Palo Alto is the traditional headquarters of the venture capital business. Sand Hill Road in particular is famous for its concentration of VC offices, and people use expressions like "the view from Sand Hill Road" to describe how VCs see the world around here. As you might expect, there are a lot of golf courses, excellent restaurants, and some really nice clubs. The Stanford campus is nice, but you'll need a bike or a car to get around (it's over 6000 acres). It is not walkable, but it is a nice place to bike.
Palo Alto has two downtown areas. There are a bunch of places catering to students which are kind of fun, like the Nut House. Palo Alto has a lot of families, at least relative to SF, and it doesn't have that many homeless. But you will probably need to be loaded to get an actual house there.
If you just want to move somewhere in the Bay Area, and you're middle class, I recommend Campbell or perhaps the Willow Glen neighborhood. There are also some nice places in the East Bay. The penninsula and SF are overpriced unless you need to be there for business reasons, or you have so much money it doesn't matter.