If you can't find a good Mexican restaurant in San Diego you aint been looking to hard. Either that or you don't know what good Mexican food is...j/k.
The best one's are the ones tucked away in the strip malls...little mom and pop joints, and there are hundreds of them in SD. Just keep trying till you find one that has all the right flavors for you, and stick with them.
As far as chains go...albertos, robertos, umbertos, roybertos, basically anything ending in bertos are all pretty good. Sergio's on Convoy is very good, and close to me so that's where I go most of the time. Good luck.