I lived in SD for 11 years (84 to 95).
Love Old Town Mexican Cafe (where else but in Old Town). Get the carnitas for 2...inexpensive and the tortillas melt in your mouth...very popular and touristy place but the locals are also there.
For the local hang out, go to Bully's East on Texas Street near the stadium. The best bartender in SD (Brad) works there. The sea food and prime rib are great and at an excellent price.
Can't go wrong in the Gas Lamp district. Too many good choices to list.