I loved the zoo I think you can see a lot of the zoo in a couple of hours by taking one of the buses that goes around. Here is a link to my gallery of the San Diego zoo. http://www.cruisemates.com/gallery2/view.php?id=613
I know you already have a hotel booked, but we really liked the Bahia Resort Hotel http://www.bahiahotel.com/welcome0.html
it is close to the zoo and has a blind harbor seal in front. The Hotel saved the seal it could not have lived in the wild. Have a fun trip.