Where are you staying? There are fun places with decent food in the Gaslamp like El Vitral and La Puerta. Fred's and Rockin' Baja Lobster have very average Mexican food with really good margaritas. Hillcrest has Ortega's for Puerto Nuevo style Mexican Food and Baja Betty's for again, average food, but great margaritas.
El Agave in Old Town has good, upscale Mexican food, but I only drink straight tequila there since they have like 100 different ones. Candelas on Coronado is much the same, upscale Mexican.
Miguel's in Coronado has a fun atmosphere, great margaritas, but again average food.
El Zarape in Normal Heights has good food and margaritas.
The best Mexican food in SD you will find is generally in places with no or limited liquor licenses.
El Zarape Restaurant
3201 Adams Ave, San Diego, CA
Rockin' Baja Lobster
3890 Twiggs St, San Diego, CA 92110
1421 University Ave, San Diego, CA 92103
560 4th Ave, San Diego, CA 92101
El Vitral Restaurant
815 J Ave, San Diego, CA 92118
2304 San Diego Ave Ste B, San Diego, CA 92110