If you're short on time, don't think you are going to be able to see everything. I've been here many times, for hours each time, and it wasn't until the seventh visit that I finally saw all of the exhibits. I recommend picking some points of interest from the map they give you at the front gate. Doing a quick rush to traverse the entire thing is just going to make your kids cranky and your feet tired.
There are plenty of cafes, of which our favorite is Albert's because there's a huge water feature out by the patio and it's very relaxing to sit for an evening meal. During the summer, they open the zoo until 9 p.m. That's the only time I've seen the large birds of prey sitting out in the open. If you're in San Diego during the summer, that might be an interesting time to come check it out. There are a lot of events going on throughout the year, so check the website to see if anything is happening while you're here.
It should be noted that I've never been a fan of zoos, but the San Diego Zoo has changed my opinion. The exhibits are large and well done. In this photo, you see a silverback gorilla holding his hands out to catch some treats that were being tossed by a keeper from above. (He gave the zoo keeper a sour look if any of the treats missed his hands.)
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Backstage Pass at the San Diego Zoo
The Backstage Pass is a custom program allowing 90-minutes of up-close access to a wide range of animals. It is a daily event that is limited to a small group of people. I think the maximum group size is 40 (the day we went there were about 25) so it is really intimate. I learned interesting things about each of the animals and had the opportunity to take some great up-close photos.