For the pumpkin cupcakes: Preheat the oven to 350 degrees F. Line one 12-cup muffin pan with paper cupcake liners.
In a medium bowl, whisk together the flour, cinnamon, ginger, allspice, nutmeg, baking powder, baking soda and 1/4 teaspoon salt. Set aside.
In a large bowl, add the butter and the sugar. Beat with a hand-held mixer until light and fluffy, 3 to 4 minutes. Add the pumpkin puree and the vanilla extract. Slowly beat in the eggs, one at a time. Incorporate the dry mixture into the wet mixtures together until thoroughly combined.
Using an ice cream scoop, fill each cupcake liner 3/4 of the way full. Bake until the tops turn golden brown and a toothpick inserted in the center of the cupcake comes out clean, about 20 minutes. Remove the cupcakes from the oven to a wire rack and cool completely before frosting.
For the cream cheese frosting: Add the cream cheese, butter, maple syrup, and salt to a large bowl and beat until creamy. Gradually add the powdered sugar until thoroughly combined.
Top the cupcakes with the frosting and chopped pecans.