Heat the oven to 350 degrees. Line 12 muffin cups with paper liners.
Whisk the flour, pumpkin pie spice, baking powder and baking soda in a medium bowl. Beat the brown sugar and oil in a large bowl at medium speed for 1 minute. Beat in ½ cup cottage cheese. At low speed, beat in the eggs, one at a time, until combined. Beat in the pumpkin. Slowly beat in the flour mixture; stir in the chocolate chips.
Divide the batter between the muffin cups. Bake for 25 minutes or until golden brown and a toothpick inserted in the center comes out clean.
Cool in the pan on a wire rack for 5 minutes. Remove from the pan and cool completely on a wire rack.
Process the cream cheese and ½ cup cottage cheese in a food processor until smooth; place in a large bowl. At low speed, beat in the maple flavoring. Slowly beat in 4 cups powdered sugar, adding the remaining powdered sugar, as necessary, for desired consistency.
Frost the cupcakes and decorate as desired; let stand until set. Cover and store cupcakes in refrigerator; serve at room temperature.