Combine lime juice, orange juice, olive oil, chipotle pepper, garlic, cumin, coriander, salt, and black pepper in a blender. Blend on high until smooth.

Pour marinade mixture into a resealable plastic bag. Add chicken breasts to the bag; marinate in the refrigerator for 3 hours.

Preheat a grill to 375 degrees F (190 degrees C).

Place marinated chicken breasts on the grill; close the lid. Discard the marinade. Grill, turning once, until chicken is no longer pink in the center and the juices run clear, 6 to 8 minutes per side. An instant-read thermometer inserted into the center should read at least 165 degrees F (74 degrees C).

Remove chicken from grill. Let stand for 5 minutes; slice into strips.

Heat tortillas over a griddle on medium heat until tortillas are soft and pliable. Stack tortillas in pairs; divide chicken, onion, and cilantro onto each pair of tortillas.