I grew up in SD. I miss it. Great town.
Some options for you to check out:
- Cabrillo Nat. Monument on Point Loma
- Take the bridge over to Coronado, not a lot to do over there but worth it for a drive. Hotel Del Coronado has been there forever and has a lot of history
- Sea World (Yeah I know, but if you've never been you should go)
- Zoo and Balboa park you can't miss - one of the best zoos in the world
- Old Town (touristy but worth a couple of hours)
- USS Midway - Don't miss this
- Gaslamp District at night
All the above is close to downtown. Head north to La Jolla and Del Mar if you want to venture a little further out. Beautiful.
Have fun!