For the waffles: Preheat a waffle iron to medium heat.
Whisk the flour, wheat germ, sugar, baking powder, spice and salt together in a large bowl.
Beat together the milk, pumpkin, melted butter, and melted shortening, egg and egg white, in a large measuring cup. Make a well in the center of the dry ingredients and pour in the wet ingredients. Whisk together to make a slightly lumpy batter.
For the topping: Melt the butter in a skillet over medium heat. Add the apples and let cook until slightly browned, but still crisp, about 4 minutes. Add the maple syrup and walnuts and toss to coat.
Pour and spread about 1 cup batter into the waffle iron. Cover and cook until crisp and a rich golden brown, about 7 minutes. (Try to resist the temptation to open the waffle iron too soon. Steam will puff out of the iron while the waffles cook, when this stops the waffle is cooked.) Repeat with the remaining batter. Serve hot with the apples.