Remove the bones from the chicken thighs while keeping the skin on by cutting two slits along each side of the bone; rinse under cold water and pat dry with paper towels.
In a large bowl, whisk together the lime juice, lime zest, olive oil, chopped cilantro, jalapeño, chipotle chili powder, minced garlic, honey, and salt until well combined.
Add the chicken thighs to the bowl and toss to coat evenly in the marinade; reserve a small amount of marinade for basting.
Cover and marinate in the refrigerator for at least 2 hours.
Preheat a grill or grill pan over medium-high heat and oil the grates or pan lightly.
Brush the chicken with some reserved marinade and grill until golden brown with char marks, about 4–6 minutes per side depending on thickness, until an internal temperature of 165°F (74°C) is reached.
Transfer to a plate and let rest briefly, then serve with lime wedges.