Make the Marinade: In a mixing bowl (or a zip-top bag), combine the olive oil, juice, and zest of 2 limes, minced garlic, chopped cilantro, honey, chili powder, pepper flakes, cumin, salt, and pepper; stir or mix until well combined.
Remove Marinade: Remove about 3 tablespoons of the marinade, place it in a bowl, cover it, and set it aside for later.
Marinate: Add the chicken thighs to the marinade and toss around to coat well; cover with plastic wrap and let stand at room temperature for 30 minutes or in the fridge for up to 2 hours.
Cook: Set a large cast iron skillet over medium-high heat and heat it until hot. Add the chicken thighs to the hot skillet—be careful, they will sizzle—and cook them for 5 minutes, or until nicely browned on the bottom; flip and continue to cook for 6 to 8 more minutes, or until cooked through. The chicken is done when its internal temperature registers at 165 F.
Finish: Remove the chicken from the skillet and let it rest for a few minutes. Brush the chicken thighs with the reserved marinade, garnish it with chopped cilantro, and serve it with lime wedges.