Prep: Grease a 9x13 pan with butter or cooking spray.
Cinnamon Apples: In a large saute pan, melt the butter over medium heat. Add diced apples and cook until softened, stirring often, about 5 minutes. Add brown sugar and spices and continue to cook for a few minutes more, until fully combined. Set aside.
Layer: In the prepared 9x13 pan, spread half of the bread cubes across the bottom. Sprinkle the cinnamon apples evenly over the bread cubes, and then the cream cheese cubes. Top with the remaining half of the bread cubes.
Liquid Mixture: In a medium bowl, whisk together the eggs, milk, maple syrup, brown sugar, cinnamon, apple pie spice, salt, and vanilla until fully combined.
Soak: Pour mixture evenly over top of bread cubes, and press down lightly on cubes until they are soaked with the liquid. Cover tightly with plastic wrap or foil, and refrigerate overnight (or for a minimum of 4 hours).
Prep: Once the casserole is ready to bake, preheat the oven to 350°F. Sprinkle pecans evenly across the top and cover with aluminum foil.
Bake: Bake the casserole for 30 minutes, then remove the aluminum foil. Continue to bake, uncovered, for about 20-25 more minutes until it is fully set in the middle and the top is golden brown. Serve warm with more maple syrup, if desired.
Store: Store the cooled casserole, covered, in the refrigerator for 4 to 5 days, or following freezing instructions below.