We stayed at The Estancia for three nights, and truly loved the beautiful hotel. I was impressed with all the succulents and the Spanish / Old California feel. After a nice dinner we enjoyed sitting and reading our book in one of several courtyards with a relaxing fountain nearby.
The hotel isn't located in a shopping area that you can walk to; the Salk Institute is just across the street, along with multiple offices and UC. In fact, many of the fellow guests were there for conferences, but it's only a 10 or 15 minute drive to downtown La Jolla and Old Town San Diego. Del Mar is even closer.
The staff is very friendly and can't do enough for you. The only downside is the hotel tax and fees, along with the valet parking, which total about $45 per day. But that's just California!