I agree with AStarOnMars, if I had to choose one I'd pick the SDZoo. Much more entertaining, better laid out, and the exhibits are newer.
The SD Zoo as a whole has better exhibits... Monkey Trails, Hippo Beach, Panda exhibit, Tiger River, etc.
Th WAP's main attraction is the monorail tour which to be honest can get a little stale if the animals are not out and about.
Just my humble opinion. Hope you a wonderful trip either way!