Be sure to include some of the adobo sauce from the can with the chopped chiles for extra flavor. Slideshow: More Casserole Recipes
Preheat the oven to 375°F. Season the chicken with 1 teaspoon salt and 3/4 teaspoon pepper.
In a large heavy pot, heat the oil over medium high heat until hot. Brown the chicken, in batches if necessary, turning occasionally with tongs, about 6 minutes per batch. Transfer the chicken to a plate. Add the onion and garlic to the pot and cook, stirring occasionally, until golden brown, about 8 minutes. Stir in the cumin and oregano and cook, stirring, until fragrant, about 1 minute. Stir in the chipotles in adobo, tomatoes and the reserved chicken with any accumulated juices. Simmer the until slightly thickened and the the chicken is cooked, about 25 minutes.
Season with salt and pepper to taste, then transfer to a 3 quart baking dish. Top the filling with the cheese and bake until the filling is bubbling and the cheese is melted, about 20 minutes. Serve garnished with cilantro.