I know very little about Mexican food but when I look at the images here I have a feeling that it is not all that genuine but all VERY American! Like pineapple on Pizza!
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That is true of Taco Bell but not El Pollo Loco. (Translated the name refers to a chicken running around with its head off, something any farmer knows about.)
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The marinade EPL uses is a family traditional recipe straight out of Mexico. The chicken is roasted over open flame, which you can see them doing when you walk in the front door. They're not hiding anything but the ingredients and spices. Not even the managers know the proportions and contents of the spice packets they get delivered. EPL roast chicken is Mexican to the bone.
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As for the side dishes, they're fairly Mexican, however, slight modifications have crept in to appeal to the American customers. You can hardly get more Mexican than Serrano chili peppers, Haas avocados, cilantro, iceberg lettuce, pinto beans, corn tortillas, steamed rice, horchata and churros for dessert. The American influence is more in the presentation, like the circular fold burrito and tall tostada shells. Their food is essentially the same as what you find in Mexico, with a little nuance of American appearance, but the ingredients are all Mexican.
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At the salsa bar EPL has whole, raw Serrano chilis. It is a very Mexican tradition to nibble on one chili while having a meal. Nothing American at all about it. Most Americans wouldn't touch them with a 10-foot pole! But if you give them a try, a little at a time, perhaps after a year or two, you will find they add a whole new dimension to the flavor of the food. They are an essential ingredient to the best guacamole, and they make pico de gallo what it is. I think they're hotter than jalapenos, but that's not a widely held opinion. They definitely have a different flavor than jalapenos -- similar but not the same. Different chilis are used for different sauces and effects.
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Even Taco Bell relies on a particular blend of chili peppers for their signature Taco Bell taste. The flagship workhorse of Taco Bell, their crunchy taco, is an American adaptation of Mexican carne asada -- uses the same spices but ground hamburger instead of chopped steak. So that's really an Americanized food item because you can't find it in Mexico, nor at El Pollo Loco! All the EPL tacos have soft shells made of corn tortillas that are NOT deep fried (like Taco Bell's are).