I used to live in SD. Rented in the La Jolla/University City area.
Check out University city(basically the area north of the 52 between the 5 and the 805). Loved the area, although the homes proved to be out of my price range at the time. But its centrally located, close to the coast, the I-5, the 805, and the 52, and its a nice, quiet neighborhood. If you can, buy a home west of Genesee Ave if you want the marine layer to hang around longer into the day, east if you would rather have the sun and a warmer day. Remember the farther away from the coast, the warmer/colder it gets. Good schools in the area.
Congrats on the move. If you can afford, SD might be the best city in the US.
Rundowns on the others:
4S Ranch - Dont know
Scripps Ranch - Nice area, a little too far from the coast so it warms up in the afternoon.
Rancho Penasquitos - Same as above
Carmel Valley - Nice, traffic sucks. I mean, traffic sucks everywhere in SoCal, but this area seemed especially prone.
Torrey Pines - Very nice, a little snooty.
Mira Mesa - Not sure how to say it, but its the truth. Looks nice, but crime rates and schools are worse because of diverse population(ie: not many white people) living in the area. Some talk of gang activity, although I never saw anything. Looked like a safe place, and we were in the area probably once a week. However, lots of locals warned us not to buy there. Just food for thought.