Cralsbad and Oceanside are closer than La Jolla but.... I used to live in Encinitas and commute to Aliso Viejo.(Orange County) I will tell you one thing whether its Carlsbad Oceanside or La Jolla it won't last. Newport is even further north than Aliso Viejo. The commute wears on you and wears on you, believe me. That drive will Kill you. Either move to Newport Beach or have your wife find another job close to La Jolla. Even if it pays less you'll be a lot happier

I don't know where you are coming from or what kind of lifestyle you are looking for so I can't suggest a location. This is a generalization but here it goes. La Jolla-wealthy types, beach and yahoo types, (Bad access to the freeway but pretty, Carlsbad-Suburbia, good schools, clean, keep up with the Jones', Oceanside-Military, Retirees, Mobile Homes, Ethnically diverse. I personally prefer Carlsbad over Oceanside and the commute is pratically the same. Oh I forgot to mention that if you live in Carlsbad or Oceanside, Your commute is shorter but literally hell driving South in the morning to La Jolla. I drive North everyday and see it. I hate to be a little negative but just letting you know the reality. If you like spending time in your car than there is no problem.
I Hope that Helped