The Park Hyatt Aviara is a really nice place but it is pretty far and inconvenient from downtown San Diego and many of the standard SAN attractions - Balboa Park, Zoo, Gaslamp, Coronado, Marine World, harbor area. I do like northern San Diego county myself but you are really making a significant choice if you stay in Carlsbad, as driving into downtown San Diego and back every day is a bit of a pain.
As the above post says, the decision is more what you want to do in San Diego than which hotel.