I lived there for 34 years, and here's what I'd recommend:
Activities:
1. Cabrillo National Monument - awesome views of San Diego & the ocean, lighthouse, history & hiking
2. Torrey Pines Glider Port - watch the hang giders, awesome views of La Jolla & ocean, a small restaurant
3. Coronado - stroll around the Hotel del Coronado, many bars & restaurants on Orange Ave., awesome views of San Diego from Coronado Shores
4. Balboa Park - beautiful parks with museums, gardens, restaurants and the the Zoo is great as well
5. La Jolla - cozy downtown area, ocean views, great shops & restaurants
6. La Jola Cove - walk along the ocean and one area has lots of sea lions that lounge on the beach
7. La Jolla Mt. Soledad - a war memorial at the top with wonderful views of the ocean and city
6. Take a tour of Petco Park(Padres) if you like baseball
9. Visit the USS Midway Museum - aircraft carrier, awesome history, right on the bay
10. Have a drink at the top of the Manchester Grand Hyatt downtown, 40th floor views
11. Pacific Beach boardwalk - lots of things & people to see, walk out on Crystal Pier, tons of bars & food
12. Embarcadero walk along the ocean, the convention center, ships, shoping, restaurants, bars
13. Hiking trails - Mission Trails/Cowles Muntain and Torrey Pines State Preserve(ocean views)
14. take a boat tour on the bay
15. Old Town San Diego - history & lots of Mexican restaurants
Restaurants:
Coasterra or Island Prime(steaks) - near the ariport, great city views,
The Fish Market - downtown on the ocean
Coronado - Il Fornaio(Italian) or Peohe's(seafood) both with great views of downtown San Doego
Downtown Gaslamp area - tons of places
Little Italy(north of downtown), bustling area with many Italian places
La Jolla downtown -
Liberty Station(just past airport near Pt. Loma) - lots of restaurants there
Nightlife:
the Gaslamp area downtown is the best, tons of bars and restaurants
Little Italy is grat as well
Downtown La Jolla is a little quieter and slower paced
Old Town, Liberty Station
Best breweries -
Stone Brewing World Bistro & Gardens - Liberty Station(Pt. Loma),
Ballast Point (Little Italy)
Eppig Brewing Waterfront - Pt. Loma