My job sent me to Tijuana/San Diego quite a bit in the past.
All of the above suggestions are good. Balboa Park is a must do if on vacation.
I have a go-to place when I am in San Diego. Not touristy, not expensive. Cap's Pizza. Neighborhood type bar on the first floor of a long stay type hotel. I like it because a) the food is good, b) its not crazy expensive, c) other than when there was a Charger's game, it wasn't packed with people.
I second Little Italy. There is a restaurant in the back of a deli that serves huge portions of awesome food. I can't remember the name of it at the moment though.
Old Towne isn't really all that much. Last time I was there two of the store fronts were turned into a giant model train layout. Not sure if it still there, but if you have any interest in model railroading/Lionel, its worth a stop. The guy was operating on donations and souvenir sales. Not sure how well it was going for him.