Preheat oven to 350degrees. In a large mixing bowl whisk together flour, baking powder, baking soda, cinnamon, nutmeg, ginger, and salt, set aside. In a separate large mixing bowl, using an electric mixer, combine vegetable oil, applesauce, granulated sugar, brown sugar and vanilla. Add eggs and stir until combine. Stir in pumpkin puree and buttermilk and stir until well combine. Slowly add dry ingredients. Stir until no longer lumpy about 1 - 2 minutes. Pour about 1/4 cup mixture into buttered muffin cups or paper lined muffin cups and bake 20 - 23 minutes until toothpick inserted in center comes out clean. Let muffins cool 5 minutes in muffin tin. Remove to a wire rack and let cool 30 minutes.
Thick Chocolate Ganache
Place chocolate chips in a medium mixing bowl, set aside. In a small saucepan over medium heat, bring whipping cream just to a boil. Pour hot cream over chocolate chips and whisk until smooth. Spoon 1 tsp ganache over each cooled cupcake and spread near edges, allow to cool. Meanwhile make spiced cream cheese frosting.
Spiced Cream Cheese Frosting
In a large mixing bowl, with an electric mixer, whip together cream cheese and butter until fluffy. Add vanilla, salt, powdered sugar, cinnamon and nutmeg and whip until smooth and fluffy. Pipe cream cheese frosting over cooled chocolate ganache covered cupcakes and sprinkle cupcakes with chopped pecans.