Add chicken, onion, garlic, 2 tbsp olive oil, honey, orange juice, chopped chipotles in adobo, 1 tbsp adobo sauce, salt, oregano, and cumin to a bowl. Toss until chicken is evenly coated, then marinate for 30 mins to 2 hours in the refrigerator.
Pre-heat oven to 425°F. Line a baking sheet with foil and set aside.
Once chicken has marinated, arrange onions on the bottom of the prepared baking sheet. Layer the chicken thighs on top, then bake for 25 mins or until chicken is cooked through.
Once the chicken thighs are cooked, remove from the oven and rest for at least 5 minutes before shredding the chicken. Note: You can pour off the excess liquid/fat from the chicken before shredding if you want. Toss the shredded chicken with onions and remaining 1 tbsp adobo sauce. Set aside.
Wipe any remaining juices from the baking sheet, then add 6 tortillas to the sheet in a single layer. Place in oven for about 3 minutes to warm the tortillas and make them pliable. You can do this twice or use a 2nd baking sheet for the remaining tortillas.
Brush one side of each tortilla with remaining olive oil, then flip the oiled side down to touch the baking sheet. To the tortillas, add chicken and cheese on one half of the tortilla, then fold the tortilla over to cover the chicken and cheese. (You may need to use a small piece of chicken to hold the tortilla closed for a couple minutes while the cheese gets melty in the oven.)
Bake for 15-20 minutes, being careful not to burn the tortillas, flipping the tacos halfway through baking time for even browning. Serve with desired toppings like guacamole, sour cream, cilantro, pickled red onions, and salsa.