1. To make Vegetables and Rice: Preheat oven to 475°F. Coat 2 large baking sheets with cooking spray.
2. Place rice and 2 cups cold water in medium saucepan, and season with salt, if desired. Bring to a boil. Reduce heat to medium-low, cover, and simmer 12 to 15 minutes, or until all liquid is absorbed and rice is tender.
3. Meanwhile, toss together eggplant, zucchini, and bell peppers with oil and chili powder in large bowl. Season with salt and pepper, if desired.
4. Spread on prepared baking sheets, and roast 20 to 25 minutes, or until tender and beginning to brown, turning occasionally.
5. To make Chipotle Tomato Sauce: Blend chipotles and garlic in blender until smooth.
6. Add tomatoes, and pulse until almost smooth but with some texture.
7. Heat oil in skillet over medium-high heat.
8. Add onion, and cook 5 to 7 minutes, or until browned and softened. Stir in tomato mixture, reduce heat to medium, and simmer 5 minutes, or until thickened.
9. Spread rice in bottom of casserole dish. Top with vegetables, then Chipotle Tomato Sauce. Sprinkle with queso fresco (if using).