Bring a large pot of salted water to a boil and cook the pasta according to package directions until al dente; drain and set aside.
In a small bowl, whisk together the chipotle chili powder, cumin, smoked paprika, brown sugar, chili powder, crushed red pepper flakes (if using), kosher salt, and black pepper.
Place the chicken in a medium bowl, toss with 1 tablespoon olive oil and half of the spice mixture; reserve the remaining spice mix.
Heat a large, high-sided skillet over medium-high heat and add the remaining 1 tablespoon olive oil. Add the seasoned chicken and cook, stirring occasionally, until browned and cooked through, about 4–5 minutes; remove chicken from the skillet and set aside.
If needed, add a small drizzle of oil to the same skillet, then add the sliced red peppers and sliced onion. Cook, stirring occasionally, until they begin to soften, about 4–5 minutes.
Reduce heat to medium, add the minced garlic and cook until fragrant, about 1–2 minutes.
Stir in the enchilada sauce, lime juice, and the reserved spice mixture. Return the cooked chicken to the skillet and stir to combine.
Add the shredded cheddar cheese and cook 1–2 minutes until the cheese begins to melt into the sauce (it does not need to be fully smooth).
Toss the drained pasta into the skillet until well coated and heated through. Gently fold in the diced avocado, if using.
Serve immediately, garnished with fresh cilantro.