I wouldn't go to San Diego it's more of a place where people live rather than vacation. But if it's already set in stone then I'm sure you guys will have a great time. I have an uncle out there and just came back from visiting with my parents and sister so our trips will probably differ but I'll tell you what we did.
We went to the botanical gardens, it was nice but not a must do by any means. We went to the harbor and saw the USS Midway, that was definitely cool and there is also a beach right there with sea lions and lots of little shops. Me and my little sister also checked out pacific beach which was definitely more of a hippie/hipster spot but it was cool being on the beach nonetheless. I saw a padres game, I always wanted to go to petco heard it was a really nice park and it didn't disappoint, also the padres suck so you can probably snag some good seats really cheap on stubhub if you buy the day of the game closest to gametime as possible. My uncle took us to this BBQ place called phils he wouldn't stop raving about, it was pretty good. We also went to the swap meet just to check it out, that was interesting. We also went to the cove, I can't specifically remember the name but it was cool.
Like I said it was a family trip so I'm sure our trips will differ. Hope you guys have fun!