Preheat Oven: Start by preheating your oven to 400°F (200°C).
Prepare Vegetables: In a large mixing bowl, combine the diced butternut squash, apples, and onion. Drizzle with olive oil, then sprinkle with salt, pepper, thyme, and nutmeg. Toss well to coat.
Transfer to Casserole Dish: Spread the mixture evenly in a baking dish and drizzle the maple syrup over the top if using.
Cover and Bake: Cover the dish with foil and bake for 30 minutes.
Add Breadcrumbs and Cheese: Remove the foil, sprinkle breadcrumbs and cheese on top if desired, and bake for an additional 15-20 minutes until the vegetables are tender and the topping is golden brown.
Serve Warm: Let it cool slightly, then serve warm and enjoy!