I grew up in SD; it's such a great town that you could spend all five days there, not do everything, and get a lot out of the trip. No matter your interest -- sea, sky, stars, beaches, shopping, sports -- you can scratch your itch in San Diego County.
Some suggestions:
- If you're going to spend a day, and only a day, at the zoo, go to the Wild Animal Park in eastern San Diego County instead of the zoo itself. Most of the animals run wild and there are some great animal shows (Best used to be the Raptor show, assuming they still do it). It's an extension of the SD Zoo, and is really a unique experience.
- If you go to the zoo itself for part of the day, spend some of that day walking through Balboa Park, which was once the home of a World's Fair and has some pretty cool art and architecture. There are lots of great museums, depending on your interests. My favorite is the Aerospace Museum which is one of the best in the country due to San Diego's long time connection to the aviation industry. The Auto museum across the street is good, but small. The Natural History museum is also good, but small (and can't compare to New York's). The Reuben H. Fleet Science Center is great if young kids are traveling with. The Museum of Man does art and anthropology if that's your interest.
- If you're giving one day to the zoo/WAP/Balboa park and only plan to spend two days, give the second to the Bay. Visit the Star of India, a sailing ship, then visit the USS Midway aircraft carrier museum, which has most of the ship and its aircraft collection open to the public. Do lunch & shopping in seaport village, and if you like take the ferry across to Coronado for some additional shopping (for more time in Coronado, visit the Hotel Del Coronado, get some beach time in on Coronado Beach, and drive down the beach at sunrise to see if you can find SEAL candidates getting some boat & log drills in at the Amphib base). Or take a harbor tour which will give you some of the history and allow you to see a lot of the giant naval base (you'll miss whale watching season unfortunately, which is best in April). The convention center (home of ComicCon) is downtown on the central bay (sadly for you, ComiCon itself is in late July). End the day by heading up Point Loma to visit the Cabrillo monument and lighthouse for sunset, then repair to Old Town for a classic San Diego Mexican dinner. Lots of Bay area sights are walking distance or accessible via light rail.
- For a survey San Diego history, visit the Gas Lamp quarter downtown (shopping, and maybe take in a Padres game), drive northeast to the Presidio and find the Mormon Battalion monument from California's brief war of Independence, then continue up to Mission Valley and visit the oldest California mission, Mission San Diego de Alcala.
- The original Sea World is in the Mission Bay area, which also has the family-friendly Mission Bay beaches and the party center of Fiesta Island.
- Walk the boardwalk and try some surfing on Mission Beach.
- Wander north along US 101 to visit the cliffs and shopping mecca of La Jolla, see the famous golf course and historic clifftop glider port at Torrey Pines, enjoy the beach at Torrey (and if feeling adventurous, walk south and strip down to enjoy historic Black's Beach the way the locals do), then continue north to enjoy Del Mar. You might be able to take in a horse race or polo at Del Mar, but the famous Del Mar fair ends in July.
- Inland adventures can include a drive up to visit the famous telescope at Palomar Mountain (great for some evening stargazing), a visit to the mountain village of Julian, the wilds of the Cuyamacas, or the beautiful Anza Borego Desert.
Shame I won't be visiting home as I'd love to tour guide.
