I've lived in San Diego (from Los Angeles though) almost a year now. How long is your trip? Here are some SD recommendations, let me know if you'll be visiting LA too!
You should definitely check out Sea World. Whales, penguins, a glass tunnel surrounded by sharks, oh my!
The historic Hotel Del Coronado is beautiful, it's haunted, the Marilyn Monroe movie Some Like It Hot was filmed there, it's where a Welsh prince met the woman he gave up his crown for, The Travel Channel named Coronado Beach as California's #1 beach, and oh yeah, my fiancé works there at the Hotel Del! The island of Coronado has a quaint, small town feel that you don't see much in SoCal and almost everything closes early.
The San Diego Zoo is famous and has pandas, but the San Diego Wild Animal Park is amazing. Instead of putting animals in cages, they actually re-created the African sarengetti where all the animals roam around. It's like watching The Lion King!
For food/nightlife check out the Gaslamp Quarter. Lots of trendy restaurants and bars, has a Farmer's Market on Sunday, adjacent to Horton Plaza mall and Petco Park.
Just west of Sea World, there's Belmont Park. It's a beachside amusement park with rides, an arcade, more food, and surf shops and souvenir shops.
In Old Town San Diego you can see "the birthplace of California" where Father Junipero Serra established the first settlement and mission. Mission San Diego was later moved, and rebuilt FIVE times, so you can skip that, skip Legoland too. Old Town San Diego still has historic buildings, living history actors, art galleries, a museum, the historic/haunted Whaley House, and a few more shops and restaurants.
Depending on where you're staying and where you're going, San Diego has a great trolley system that visits many (but not all) attractions. It will take you to Downtown, Gaslamp, Old Town, within walking distance of the zoo and Sea World, the stadiums, and lots more shopping and dining. It won't take you to Torrey Pines, the Hotel Del Coronado(accessible by bridge, ferry from downtown then local bus on Coronado island, or the Silver Strand), or the Wild Animal Park so you should rent a car at least a couple days.
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