I'm assuming the beach is on your list somewhere?? The beach is free and provides *endless* entertainments for the kids.
I grew up in SD and we just visited as tourists with the kids in Oct. We made a point of going to SeaWorld since they have Shamu; it was a hit. Otherwise we mainly visited the beaches and the kids were ecstatic.
La Jolla Shores: Big, long beach with nearby restaurants. Lots of room to play. Lots of parking
Scripps Beach: right next to La Jolla Shores, but when the tide is low you can visit the tidepools. If you stop at the Birch Aquarium on the way to the beach (they open at 9) you can learn about shore life and then go see it in person. How cool is that?
Coronado beach: HUGE wide open beach. Can visit Hotel Del Coronado or Star of India if they want to see a pirate ship, or USS Midway the big Aircraft Carrier on the way.
Swami Beach: Nice gardens nearby, huge cliffs, lots of fun.
Solana Beach: small intimate beach, there is a playground right near the entrance.
Del Mar: has a dog beach. It's fun to watch the dogs play
Childrens Beach in La Jolla: watch the seals and sea lions
Ocean Beach: Quirky people, near Sea World
The Zoo is very, very nice. But it's built on a hill so there is a LOT of up and down. And to be honest, it's the same animals you'd find at any zoo. For the price, IMHO, it's just not that worth it.
The only thing I will warn you of: May Grey and June Gloom. SD gets it's gloomiest weather in Apr/May/June. The clouds build up overnight and it takes until midafternoon for them to burn off. July/Aug/Sept thru Mid Oct are the nicest months to visit since it's so sunny.
For restaurants. Roberto's is the best cheap mexican food ever, lots of locations. El Indio on Grape St near the airport. Chicken Pot Pie Shop in Hillcrest -there are tons of great other restaurants there too. The cheese shop in LJ Shores and Downtown. It's an icon.
Have a good trip!