Zest the lemons first, then juice them to capture all the bright citrus flavor. Mince the shallot and garlic cloves finely so they distribute evenly throughout the marinade. In a bowl, whisk together the lemon zest, lemon juice, minced shallot, minced garlic, olive oil, oregano, salt, paprika, pepper, and red pepper flakes. I always make sure the garlic and shallot are finely minced because larger pieces won't infuse the marinade as effectively. Finely chop the parsley into roughly 1/4-inch pieces and set aside for garnish.
Pat the chicken thighs dry with paper towels to help them absorb the marinade better. Place the thighs in a bowl or zip-top bag and pour the marinade from Step 1 over them, making sure each piece is well coated. Cover or seal and refrigerate for 1-2 hours. This time allows the lemon, garlic, and herbs to penetrate the meat and develop deeper flavor.
Remove the chicken from the refrigerator 10 minutes before cooking so it comes closer to room temperature for even cooking. Heat a large skillet over medium-high heat until it's hot but not smoking—about 2 minutes. Working in batches to avoid crowding the pan, place half the chicken thighs skin-side down (or presentation-side down if using boneless), letting them sear undisturbed for 5-6 minutes until golden brown. Flip and cook the other side for another 5-6 minutes until the internal temperature reaches 165°F. I like to let the chicken develop a nice golden crust before flipping because it helps lock in the juices.
Transfer the first batch of cooked chicken to a serving platter and keep warm. Repeat the searing process with the remaining chicken thighs in the same skillet, cooking 5-6 minutes per side until they reach 165°F internal temperature. Once all chicken is cooked, arrange on a serving platter and top generously with the chopped parsley from Step 1. Drizzle any remaining pan juices over the chicken for extra flavor.