So many choices. San Diego has limitless choices. If you love the beach, take your pic. There is the laid back Encinitas/Leucadia area. There is the up and coming Oceanside area and the uber-expensive and personal favorite Del Mar. The commute sucks though.
If you love the city. La Jolla is a world unto itself though its citizenry is unfailingly stuck on itself and its always kinda cold. Clairemont has lots of options, as long as you want a 1950’s stucco box with an extra 1000 square feet of house, unpermitted. It is however centrally located.
Poway, ah yes the country in the city. I went to high school there, though never lived in it. It used to be that Poway was somewhat isolated from the rest of the city you had to get off the freeway and kind of hunt for it. Alas no longer. It has grown to be a rather large suburb. Good schools decent houses, but not many jobs. I seem to remember it being a horse friendly town, though I imagine that is changing.
Sorrento Mesa/UTC, sterile.
Countryside anyone? I suppose Valley Center, my childhood home still qualifies. Not a good choice though if you have gambling issues. I hear they have quite a few casinos now. Plus its full of Mormons. It is beautiful and the sunsets cannot be beat. Again the commute will be a bear, unless you want to make very little money then Escondido is an option.
Julian is beautiful, somewhat isolated and very rural. I have only actually gone there a few times, mostly after paragliding at Mt Laguna, but it has a quaint charm. That is unless you own a large truck or SUV and have to drive into the city to work.
I think almost any part of San Diego can be a good place to raise kids. There are execptions, but no place is perfect.
Those are just a few, as I said this place has so many options.