I confess that I will be biased, having lived in San Diego for 7 years, always less than a block from a real Mexi-Cali style restaurant, with authentic Mexican flavor (and authentic Mexicans!). Taco Tonto's is good, but it's not very authentic. It drives me crazy that the larger burrito is called "El Biggo." Or that the taco salad-y thing I ordered came served on stale, round, grocery-store-style tortilla chips, and not on a crispy corn tortilla. But those gripes aside, the other food I've tried is decent (especially the chicken taco), the prices are reasonable, and the atmosphere is friendly. Just be prepared to wait forever for your food to be ready - no rushing here.
When the weather's good, it's even more enjoyable to buy a drink at Zephyr, sit on their patio, and enjoy your tacos there via the pickup window.