Hornblower Cruises off harbor drive can take you on whale watching tours, and there is the Torrey Pines National Park and Cedar Creek Falls if you are into nature hikes
Seaport village makes for a nice afternoon. There is just about always some street performers doing there thing. Just a short drive away is the Midway aircraft carrier as well as Star of India.
Cabrillo monument in Pt. Loma is pretty cool, great views of N.I. and the Sub Base, it is fun to watch the Navy ships pull in and out. While you are out there head down the hill to the tide pools there is never many people out there and some amazing sunsets.
Santee lakes are pretty fun to spend some time at, can fish without a license and rent a paddle boat and feed the ducks.
if you like the outdoors you can always hit up Mission Trails. great place to walk hike or bike! just off the 52 on mast or you can get on mission gorge from the 8 or 15 and head east.
WAP or what ever the new name is, the Zoo, Seaworld, legoland, quail botanical gardens, balboa park(musems, and botanical garden next to the zoo), midway musem is great so is the star of india next to it, old town, birch aquarium, legoland aquarium, cabrillo monument and the tide pools below, also the Fort Rosecrans Cemetary is also very humbling.
Seals/sea lions in La Jolla.
Lighthouse area around Point Loma.
Soak City in Chula Vista in the summer.
Legoland.
Beaches, beaches, and beaches.
On my bucket list- Egg Shamu. I need security details on Sea World. This will have to be a covert op with lots of recon.
Julian.
Fish the Coronado Islands.
Balboa Park.