Lightly grease a 12 inch skillet, Cook spaghetti according to package directions in a pot of boiling salted water. Drain, rinse, and transfer to skillet.
Place tomatoes, jalapenos on a foil lined baking sheet, skin side up along with the garlic cloves and onion Broil 5 to 7 minutes on a rack placed 6 inches from heat. Remove from oven let vegetables cool, dice. Reduce oven to 350 degrees.
Melt butter in a sauce pan over medium low heat, Whisk in flour until well combined and slightly browned about 30 seconds, slowly pour in milk and cook stirring until sauce thickens to coat spoon 3 to 5 minutes.
Turn off heat and slowly stir in half the cheese about 1/2 cup at a time until melted into sauce.
Stir in diced vegetables along with cumin, cayenne, cilantro, and lime juice add salt and pepper.
Pour sauce into cooked spaghetti and stir in shredded chicken. Top with remaining cheese.
Bake uncovered 20 minutes or until brown and bubbling. Sprinkle with cilantro serve.