Whisk together first 5 ingredients in a shallow dish or zip-top plastic freezer bag; add chicken, turning to coat. Cover or seal, and chill 30 minutes to 3 hours.
Preheat oven to 375°. Lightly grease a 13- x 9-inch baking dish. Remove chicken from marinade, discarding marinade. Place chicken, skin sides up, in prepared baking dish. Bake at 375° for 40 minutes or until done and skin is golden brown.
Meanwhile, pour oil to a depth of 2 inches into a Dutch oven; heat over medium-high heat to 350°. Lightly dredge shallots in flour, shaking off excess. Fry shallots, in batches, 1 to 2 minutes or just until crispy. Drain on a paper towel-lined baking sheet. Repeat procedure with garlic and jalapeño pepper. Sprinkle shallots, garlic, and jalapeño pepper generously with salt and pepper to taste.
Divide chicken among individual serving plates. Sprinkle with shallots, garlic, jalapeño pepper, and cilantro. Serve immediately.