SD is a very family friendly area M.:)
Go to both early morning..still dewy and also, night time!! if you think your kids would like it.
Consider a City Pass or Go Card
http://www.travelforkids.com/Funtodo/California/San_Diego...
We are HILTON rewards people and the Hilton Mission Valley but if you want beach, there are others...this one is central to all freeways that head this way and that.
YUMMMY~
Tons of restaurants but this one is unique, affordable, quick for the kids and a lot of quality..several locations
http://www.patandoscars.com/
Zoo...my humble suggestion. I am not a marathon runner but was disgusted by people standing in line to ride a bus...unwilling (not about ability issues here) to avoid walking LONG LINES..you will be half way through the park while people wait in line...eating junk, getting more unhealthy .Buses never get close to the animal after a long line.
.You will get some walking in but feel great after..Your kids wil get a much better experience too..and you will not be loading on and off a bus...
Bring bathing suits and towels and a plastic shawl to Sea World so the kids can play in the water area but if you do not want to get wet with Shamu, you are covered..
There is also a sand area....nice as an energy burner before hotel night night
Avoid overly crowded beaches, just frustrating. I love to go to beaches in OC as I used to live there. Email me if you want suggestions. If you are driving, I would make one stop OC..Newport or LB, even San Clemente or Dana P.