I second Encinitas. I work in La Jolla, and live near Birmingham in Cardiff, and exit at Genessee and rarely does the morning drive take more than 25 minutes. The afternoon drive is generally about 30 minutes. So the downtown drive would probably add 20 minutes or so.
I see a lot of houses for rent east of El Camino Real, between Encinitas Blvd. and Leucadia (Rancho Santa Fe Rd.) making it quite easy to move when you are ready and stay within the same schools. The Park Place area of Cardiff is very family oriented, and has a good mix of rental and for sale homes, and you wouldn’t have to switch schools.