well you didn't mention seaworld so I am assuming that you have decided not to go there, but we just went recently with my daughter (3) and she LOVED it - if you have little ones, they have an all new play area just for kids thats a lot of fun and my daughter really really liked feeding the dolphins and manta rays. One of my favorite moments of the whole trip was her reaction to the shamu show - she was mesmerized!
There is also a great deal that you can get through costco that includes sea world, san diego zoo and the wild animal park for a decent discount - supposedly the wild animal park is awesome, though we didn't make it out to it last trip.
Balboa park is supposed to be a really cool day trip type thing too - lots of neat museums and they just opened an all new children's museum in san diego also.
Good luck planning and have fun!