For a great romantic dinner with the best view of the downtown skyline, go to Pehoe's in Coronado. You can take the water taxi across the harbor.
http://www.peohes.com/
http://www.sdhe.com/san-diego-water-taxi.html
La Jolla offers great views, great surfing, great food, great theater, and great shopping.
Take a stroll on Prospect St and check out the shops, galleries, and have some authentic Mexican food at Alfonso's. Jose's Courtroom is where the locals hang out to drink and eat. The Spot offers Chicago style food with both deep dish and thin crust pizza. For gourmet cuisine, it's George's at the Cove.
http://www.alfonsosoflajolla.com/
http://joses.com/
http://thespotonline.com/
http://www.georgesatthecove.com/
The Mandarin House in La Jolla features home made noodles and some of the best Chinese food in town. It's located one block from the world famous Windansea Beach. Check out the surfers and take a sunset stroll. Then have dinner. December is the ideal time to walk out onto the tide pools. It's the lowest tide or the year and just north of Windansea there is an enormous area that becomes accessible at low tide. You might even get a peak at Mitt Romney's new house.
http://mandarinhousesandiego.com/
Old Town has one of the best Italian restaurants in town. Pizza Bella features home made Italian food made from Mama Bella's recipies. During the day their courtyard is open for outdoor dining. It's one block from the Old Town trolley stop.
http://www.yelp.com/biz/pizza-bella-san-diego
Closer to downtown and one of my favorites is El Indio. Serving Mexican food since 1940, it's a short walk from the Washington St. trolley stop.
http://www.el-indio.com/
Serving breakfast since 1960, Harry's Coffee Shop in La Jolla is an institution. Everyone goes to Harry's.
http://www.yelp.com/biz/harrys-coffee-shop-la-jolla