Wild Animal Park is great too. I second all of the suggestions as well.
Del Mar and La Jolla are great places for lunch, but dinner would be pricey with younger kiddos.
As far as Mexican food: Old Town Mexican is one of the better ones, but for authentic, hit up Las Cuatras Milpas for lunch. It's in the barrio and everyone lines up there for lunch. Cheap authentic, non-Americanized food. Check out Lucha Libre too. They have a website. Its a small place set up all in Mexican wrestling kitsch. Good food and your kids will dig it.
For a day trip, go up to Julian, an old mining town and/or continue on to the desert. You can do the beaches, mountains and desert all in a day here.
Birch Aquarium is good, but after Sea World your kids will likely be unimpressed.
Balboa Park is worth at least a walk through when you do the zoo.
I just took the train up the coast a bit. You can take it to San Juan Capistrano for an interesting visit to a California Mission...theres an awesome playground for a picnic right behind the train station if you want to truly daytrip it.
Definitely go to Coronado and seee the Hotel Del Coronado. Such a fun place to visit and there are good beaches there too. If you want to splurge, have brunch there on the weekend. You can drive over the bridge or take the ferry.
Beaches: Coronado is good, as is La Jolla. La Jolla has a snorkeling cove with classes to take. Pacific Beach is young and Ocean Beach is the grungy smoker scene. Mission Beach has both a beach and bayside as well as an old roller coaster that is fun.
If you can hit the zoo as soon as it opens you will see more animal activity aand the least visitors. The opposite is true od the Wild Animal Park. On a hot day, hit the animal park at the rnd of the day and take the last tram ride. Fewer people and more animals.
Finally, if you want to see any great examples of California gardens, check out the free Water Conservation Garden at Cuyumaca college. It has gorgeous succulent gardens and California native and friendly plants. The Quail Botanical Gardens are also great...but coastal, so different plants. There is an awesome bakery called Elizabethan Desserts right near there tucked in a nursery which has the best non-commercialized cupcakes you will ever eat.
Enjoy your trip. I was born and raised here and after 5 years in L.A.....ugh..am back to raise my kiddos here! Feel free to send me a private message. I'm chock full of opinions and ideas on SD! :)