In a large mixing bowl, toss the sliced chicken with chili powder, garlic powder, cumin, and ½ teaspoon of salt, coating the chicken evenly with the spices.
Heat 1 tablespoon of olive oil in a large skillet over medium-high heat. Add the seasoned chicken and cook for about 6 minutes, stirring occasionally, until fully cooked. Transfer the chicken to a clean bowl.
Using the same skillet, sauté the diced red bell pepper and onion until they become tender and slightly caramelized. Stir in the minced garlic and cook for an additional 30 seconds. Transfer this mixture to the bowl with the chicken, then add the minced chipotle peppers, 1 tablespoon of adobo sauce, and chopped cilantro. Stir until well-combined.
In a small bowl, combine Greek yogurt, lime juice, remaining ½ teaspoon of salt, and the remaining 1 tablespoon of adobo sauce. Set aside as a dipping sauce.
Heat a large skillet over medium-low. Sprinkle ¼ cup of shredded cheese over one side of each tortilla. Spread ¼ of the chicken and pepper mixture on top of the cheese, followed by another ¼ cup of cheese. Fold each tortilla in half to enclose the filling.
Lightly coat the skillet with olive oil and place a quesadilla in the pan. Cook for 3-4 minutes on each side, or until the cheese has melted and the exterior is golden and crisp. Remove from the skillet and let rest on a cutting board for 2 minutes before slicing into thirds.
Serve warm with the chipotle Greek yogurt sauce and additional chopped cilantro if desired.