M.J.
I've lived throughout the South Bay and could never afford Palo Alto. Is it a great place to live? Absolutely. But a 3 br. home is going to cost a fortune. You're in the million+ territory. Definitely places to walk and bike in the area. Public transportation is available but not too many people in that area would use it, other than students. This is a city where most people drive a Mercedes or similar vehicle.
What's great about the area? A lot of educated people. Innovative industry. Best weather in the country. Tons to do. If you're outdoor people, this is a super area to live. People are very active and you'll find lots of places to hike and bike. The fantastic weather allows you to be outdoors a lot of the year.
You're going to want to look up the Peninsula to areas like Redwood City or south to San Jose to get more affordable housing. Schools will depend on the specific neighborhood you select. The more expensive, the better the schools. Definitely find a realtor who can help you narrow it down.