What would you do in the San Diego area...
Where are you coming from, what time of year will it be and what do you like to do?
Balboa Park is nice - lots of museums that are fun for a two year old, the zoo, playgrounds, lots of open space and paths, a couple of nice restaurants and places to have a snack or a coffee. No beach or ocean view, though.
Coronado Island is nice, there is a beach, shops, a little town area. There is a ferry boat that goes there from the downtown area, or you can drive over the bridge to get there. It's beachy.
Downtown La Jolla is nice to walk around in. It perches right on the ocean, so you can walk along the cliffs, look at the seals, run on the sand, and have a nice lunch or go to the playground at the Rec. Center.
North County has some nice beach towns also. Del Mar has Powerhouse Park which has a playground and is close to the train tracks if your 2 yo likes to watch trains pass by. It's right on the sand, and walking distance to shops. Close by is Torrey Pines State Reserve where you can hike with ocean views.
There are lots of nice places to spend the day outside.