Mexican food in the greater San Diego area:
There's certainly no shortage of great Mexican food there.
Is there anything in particular you're looking for? Have you been to Oaxacan places? Mariscos places?
There are plenty of choices which don't involve a pound of melted cheese on the beans.
If you want something beyond the usual gabacho-friendly choices, try getting out of the gabacho neighborhoods. If you hear a lot of unaccented English, it's a warning. English in general, directed to anyone other than you, is also not a good sign.
If you choose anyplace which does a big margarita trade at happy hour, you deserve the food.
If you choose anyplace located within an "historic district," or any other touristy destination, you deserve the food. Giant malls aren't usually happy hunting grounds either. Strip malls, on the other hand, are. Any restaurant within two strip malls of a large Mexican market -- especially if there are other restaurants as close -- is a decent wager.
If you insist on prissy levels of cleanliness, you will unnecessarily limit your choices.
Look for places advertising "tortillas hecho a mano, that's not a sure bet, but it's a start. If they advertise mariscos, cocteles , cheladas, micheladas, jugos frescos, and/or licuadas as well, you're half way home.
Start drinking cheladas.
Don't be afraid of stereotypes, as long as their accurate. Look for places where a high percentage of the men are wearing straw "cowboy" hats. Women with braids -- each hair as thick as rope is good. If it's grey hair with one long fat braid down the center of the back, even better.
Embrace offal.
You're asking in the wrong place. Join chow.com -- peruse the threads already there, then post the same ol' same ol' questions and get fresh answers from new people. Yelp can be helpful, but Chow is better.
If you're asking, "What's a gabacho, you're a gabacho. Worse, if you think you might be a gringo, you're the epitome of a pinche gabacho. H/t "Ask a Mexican."
Get in touch with your inner sureño, you'll be fine.
BDL