I assume you’ve done or considered the other tourist things like Old Town, Gaslamp Quarter, Mission Beach, and Coronado? Head over to Liberty Station for lunch in the Public Market food court area and get a great view of the city. Go up the coast by commuter rail to Carlsbad or Encinitas for food/beach walk. If you have a car and time, take a road-trip to Julian in the mountains. The Instagram account, Hidden San Diego, posts info on cool off the beaten path parks, hikes, and historic areas.
I liked the Hop on Hop off bus tour and really really liked the Harbor Tour. Wouldn't think it would exactly be my thing, but the USS Midway tour was amazing and so glad we went early because we were there all day.
If going to Tijuana, remember you need a passport and the real concern would be returning to the US. Whether driving back or walking back, there could legitimately be a multi-hour line of traffic to come back to the US. (Though a physical global entry card would help, if driving)
check the tide charts, has to be low tide, to walk from Torrey Pines beach to the Scripps Pier, through Black’s Beach, aka nude beach, mentioned here. You’ll deserve drinks or dinner at La Valencia after that
Old Town is fun (great food there), Hotel Del Coronado has the best beach, Gaslamp and Little Italy has fun bars and restaurants, Liberty Station (especially Corvette Diner), and more. San Diego has some fun theater and music areas (like Humphrey's in Shelter Island for Jazz). My favorite place to recommend is called Extraordinary Desserts near Banker's Hill. La Jolla is a relatively wealthy area with great beaches and shopping. Check out when the Del Mar Fair opens as they have lots of fun bands and more.