I haven't been to Sea World in a while...I know the Zoo a lot better.
If you don't mind walking, my recommendation is to get to the Zoo right after it opens and go down Tiger River and see the tigers, then see the pandas (if you're there early you might actually see them moving/eating rather than just sleeping!) and then see the cats/small carnivores in Cat Canyon, since they are also more active in the morning. After that you might want to take the bus tour (if you're planning to do that), and that gives you a good overview of things you might want to go back and see later. You get a much better view of the koalas by going to the exhibit than you do from the bus, and the Polar bears are also best viewed at the exhibit. You also can't see the gorillas, orangutans and other monkeys from the bus, but at least that exhibit is just inside the front entrance to the Zoo so it's easy to get to. The Children's Zoo is fun (even if you don't have kids), and I really like the Wild Ones show in the Hunt Amphitheater. I've not been too impressed by the food at the Zoo, though it has improved a bit...Sidney's Grill is decent, as is the place down near the gorillas. But I think the burgers at the burger stands are like cardboard.
Places to eat in San Diego - there are tons!!! Depends on what you like...seafood, Italian, Mexican, American, etc. and how much you want to spend. There are lots of nice (and somewhat pricey) restaurants down in the Gaslamp District downtown. Anthony's, right on the harbor serves decent, and reasonably priced, seafood. Humphrey's, on Shelter Island, is also good. The Prado restaurant in Balboa Park is quite good for lunch - I haven't had dinner there.
If you want to try more "local" flavors...try the fish tacos at any of the many Rubio's fast food places around town. Or the Mexican food at many of the Roberto's fast food places. On India Street, try Filippi's pizza grotto - it's an Italian restaurant that's behind an Italian grocery store - it's a local fixture, and has been there for years. Also on India Street, but further north, is El Indio's, a take-out Mexican place. They used to be really good, but not quite as good recently, though their fresh tortillas (they make them there) are still awesome. Just down the street from El Indio's is Saffron, a little hole-in-the-wall Thai place, but the food is terrific. Both those places have seating available - El Indio's is outdoor, and Saffron has some inside, some outside.
There's many restaurants in Old Town. Old Town Mexican Cafe is another place that's been there for years, and has good Mexican food (their carnitas plate is quite good). Rockin' Baja Lobster and Guadalajara Grill tend to have more run-of-the-mill chain-restaurant-style Mexican food, but it's decent.
Hope that helps.
