I live seriously like 5 min from the zoo. I personally think the zoo is better for the following reasons.
1. there is far much more to see and do at the zoo
-more shows & more animals to see.
2. it is NOT nearly as hot as the wild animal park aka safari park
3. it is right next to Balboa park and all the meuseums
4. it is next to the little art villiage
5. it is centrally located in san diego and next to downtown
when you are visiting san diego i also recommend going to
sea port villiage
old town (see the famous waley house)
sea world
balboa park
coronado island (hotel del)
rancho bernardo winery ($5 flight of wine & you get to keep the glass)
Petco park
gaslamp in downtown
The light house in point loma
places i recommend to eat
phils bbq (an absolute must) in point loma
wines steals in point loma
forever fondue in la jolla
city deli (hillcrest)
hope you enjoy your trip to san diego