They are different experiences. The Zoo is great - huge too. The newer areas are really nice for the animals - and they have lots of animals. The WAP isn't as big and doesn't have the variety of animals the Zoo has, but it is arranged really nicely and you can get closer to the animals - while at the Zoo I've found often the animals are hiding and hard to see. The silverback gorilla exhibit is fabulous at WAP - and there is a family of lions that sometimes gets very close to the glass exhibit wall - they like to hang out (literally) on a jeep that's there! You can feed giraffes sometimes as well. WAP also offers some real close-up opportunites if you want to pay $$ - like photo caravans where they'll drive you right up to some of the animals in the large open area of the park.
I've had APs to both for a number of year ( 1 AP as said before gets 2 parks). I tend to take out-of-town visitors to WAP instead, because it's not a traditional Zoo. But it does have less to see overall - you can see most everything in 1/2 a day, while the zoo takes a full day ( some spent trying to find those hiding animals!) The zoo does have the pandas - and you get surprisingly close to those - and a couple of very fun polar bears, and some koalas. If you have some favorite animal you may want to check with their website to see where you are more likely to find them. The layout of WAP IS more like the AK, but without all the cool theming and rides. One other interesting thing about the zoo is that the value of the landscaping is greater than that of the animals - so if you're into plants, that might influence your choice.
So it's a very personal choice - but if you have access to local good zoos, I'd pick WAP. But: it's not really in San Diego - it's in Escondido, which is further north and very much more inland ( and hotter!). The Zoo is in the middle of town, and in a fabulous park with other museums,theaters and lovely walkways. So if you want to see San Diego, pick the Zoo!
