Preheat your oven to 350 degrees F. Spray a 9 x 13-inch baking dish with cooking spray. Set aside.
In a large skillet, cook the ground beef over medium heat. Break up the beef and continue to cook until the beef is no longer pink. You can drain off some of the excessive grease if you like.
Add the diced onion and green peppers to the beef and continue to cook for about 5 minutes or until the vegetables are softened.
While the vegetables are cooking, boil the spaghetti as per the package directions until al dente. Drain and set aside.
Add the chili powder, cumin, paprika, red pepper flakes, garlic powder, onion powder, Kosher salt, and fresh ground pepper. Stir to incorporate the seasonings.
Add the green chilis, the can of Rotel tomatoes, and the tomato sauce. Reduce the heat to low and simmer for about 15 minutes until reduced slightly.
Place the cooked spaghetti in the bottom of the baking dish and spoon the meat sauce over the top of the spaghetti. Even out the sauce to the edge of the dish, making sure that the spaghetti is completely covered.
Sprinkle the grated sharp cheddar cheese and grated Monterey Jack cheese over the top of the meat sauce.
Place in the oven and bake for 15 minutes or until the cheese is completely melted.