Hey Chief, I'm raised in San Diego. TrickBlue recommended that one Mexican restaurant in Old Town - unfortunately, the owners of Old Town sold it in May and all the cool Mexican, open-air restaurants had to move out. Here's my recommendations:
1. Besides the combination of Shamu, the Zoo, Wild Animal Park, up to Disneyland.
2. Padres game at PetCo. Park - Park at the Park is $5, I think. It's entrance to the lawn in the outfield. You can bring a picnic blanket and watch the game from there. That's one special thing you can do besides get regular seating.
Heart of Gaslamp Quarter is about a 15 minute walk to Pet Co Park. So, you can check out Gaslamp Qtr all day, then walk to a night game. Gaslamp Qtr is the redeveloped downtown district, typical of lots of American cities redeveloped downtowns. Very busy clubbing place at nighttime with the young and more mature crowd. Horton Plaza is a major shopping mall (Macy's, Banana Republic) inside the Gaslamp. Lots of upscale restaurants there.
3. Deep-sea fishing at H&M Landing or you can go to Coronado Island and rent a small speedboat for a couple hours out in the bay
4. La Jolla Cove - upscale beach neighborhood and commercial area. Children's Pool is a beach that has seals on it and a great place to watch the waves crash. Walking around Prospect Drive/Avenue/Rd (forgot which one) is nice. Has some shopping, really chichi-lala restaurants like George's At the Cove. Pretty quiet with some commercial places to shop, but a great place to watch the sunset.
5. Pt. Loma tidepools - check times for low tide then go there. You can see little crabs, starfish, little fish, eels, mollusks and other little creatures that get stuck in the rock formations full of water when the tide recedes.
6. go to Tijuana, Mexico during the day - cheap eats, flea market shopping. It's another country. If you drive, border waits are unpredictable (30 minutes to 2 hours). I recommend walking across, but it's a lot of walking.
7. Pacific Beach is the urban, beach community. Younger beach crowd, clubs at night, lots of bars and surfboard rentals shops. You'll see college-aged girls walking around in bikinis, lots of boutiques and different restaurants that are affordable. At nighttime, this place gets taken over by college partiers. Good place during day, but too wild for kids.
Drive up the 101 around Encinitas for quieter beach community with convenient surfboard rental shops and some local restaurants (like Pizza Port) but at night it's quiet.
8. Pretty much any Mexican restaurant is good. You simply pay for the ambiance and diversity of menu. Small taco shops like Roberto's are just as good as the more expensive places. Avoid El Torito and Chevy's - food okay, but more bang for the buck elsewhere.
9. Del Mar Fair/San Diego County Fair/Del Mar Fairgrounds - horse-race betting and the largest carnival fair (roller coasters, cotton candy, the works) just started last week for the summer months. Great place for kids and to bet on horse racing! I highly recommend.
10. Avoid driving north of the 805/5 highway merge between 4-6pm. Avoid the 805 driving south on the 805 hwy between 3-6pm.
11. Hillcrest - the gay community. Has lots of nice boutiques and Thai, sushi restaurants. Phil's BBQ on Goldfinch has the best ribs - limited seating and about 30 minute wait. Corvette Diner - 50's themed burger joint. I recommend the Peanut Butter Burger.
12. Indian Gaming Casinos - Viejas, Barona and others are like 1 hour drive east of San Diego. Great outlet shopping centers. Kids under 18 can't gamble, of course, so up to you. Only if you still have time.
13. Coronado Island - other than the scenic drive on the Coronado Bridge, there's not too much there to do or shops. Very quiet, rich neighborhood. Nice beach, but same thing with other beaches. I don't really recommend it.
14. For the kids - Ruben H. Fleet Space Theatre - they have an IMAX theatre that shows lots of educational/nature films. I enjoyed that as a kid. In Balboa Park, which also has the Natural History Museum and Museum of Man and other museums.
To avoid - no need to go south of downtown. Mission Valley/Fashion Valley is where the biggest malls and Jack Murphy Stadium are. Nothing special there but shopping, which you can do at Horton Plaza in the Gaslamp. Avoid any chain restaurants like Outback Steakhouse, Chili's, Applebee's. There's plenty of local restaurants. Beware of Pacific Beach and Gaslamp Qtr at night because of your kids and all the partiers.