In addition to everything that has been mentioned, I would recommend a dinner cruise of San Diego Bay.
Check out Hornblower Cruises:
https://www.hornblower.com/port/category/sd+diningcruises
The Birch Aquarium in La Jolla:
https://aquarium.ucsd.edu/
The Museum of Making Music in Carlsbad:
https://www.museumofmakingmusic.org/
See a show at the elegantly restored Balboa Theater:
https://theater-sandiego.com/balboa/?gclid=CjwKCAjw7_rlBRBaEiwAc23rhticoW1jSoVzKhOu8Sw3UFO-9skqElgIaNSkyruoCplyf1WmxbCPAhoC24gQAvD_BwE
Have lunch at Liberty Public Market at Liberty Station:
https://bluebridgehospitality.com/libertypublicmarket/
Go to one of the several Indian casinos to gamble, or eat at the buffet, or both, that are all within a half hour, to an hour and a half drive from Downtown San Diego including Pala, Pauma, Harrah’s Rincon, Valley View, Sycuan, or Viejas.
If you are going there in June or the beginning of July, go to the San Diego County Fair:
https://sdfair.com/
Have a casual breakfast or lunch alfresco at the Cliff Hanger Café, high above Blacks Beach and watch hang gliders and parasailers jump off the cliffs at The Torrey Pines Glider Port:
https://www.flytorrey.com/the-cafe/
Right behind the glider port is the campus of UCSD. If you like public art and interesting architecture, you can see the iconic UCSD Library building, and the University’s Stuart Collection:
http://stuartcollection.ucsd.edu/
Eat a fish taco (at pretty much any taco stand, or Mexican restaurant in San Diego), but if you want to eat one at the official birthplace of fish tacos in San Diego go to Rubio’s #1 at Mission Bay, and then enjoy yourself at the beach at Mission Bay:
https://www.rubios.com/restaurant-locations/california/san-diego/mission-bay
Visit the meditation garden at the Self Realization Fellowship Temple in Encinitas. It’s free to the public, and no one will try to indoctrinate you. It’s a plant lover’s haven that sits high above Swami’s beach, one of the best surfing spots in San Diego County:
http://www.encinitastemple.org/visiting/
Then have breakfast or lunch at Swami’s Cafe (across the street on highway 101):
http://swamiscafe.com/
If you like 50’s era diners, and the ocean, head to Ruby’s Diner on the pier at Oceanside:
https://www.rubys.com/locations/oceanside/
Get up to the Cuyamaca mountains, about an hour East of downtown San Diego, and visit the quaint, former gold mining town of Julian,and treat yourself to some famous apple pie, and see breathtaking views of the Anza Borrego Desert below, to the East:
https://www.sandiegofamily.com/travel/family-visit-to-julian
Stay at the Orchard Hill Country Inn Cottages:
https://www.orchardhill.com/
Ot The Julian Lodge:
http://www.julianlodge.com/
Have a great trip : )