Preheat oven to 350 degrees F. Grease and lightly flour twelve 2 1/2-inch muffin cups. Or line cups with paper baking cups and lightly coat cups with nonstick cooking spray; set aside.
In a large bowl stir together flour, flaxseed meal, baking powder, pumpkin pie spice, baking soda, and salt; set aside. In a medium mixing bowl lightly whisk eggs. Whisk in pumpkin, agave nectar, and oil. Add pumpkin mixture all at once to flour mixture. Stir just until combined. Spoon batter evenly into prepared muffin cups.
Bake for 18 to 20 minutes or until a wooden toothpick inserted in centers comes out clean. Cool in pan on a wire rack for 5 minutes. Remove cupcakes from pan; cool completely on wire rack.
Spread Cream Cheese Frosting evenly on cooled cupcakes. Garnish with freshly grated nutmeg. Serve immediately or store cupcakes in an airtight container in the refrigerator. Serve the same day they are made.
Cream Cheese Frosting
In a small mixing bowl combine reduced-fat cream cheese, agave nectar, butter, and vanilla. Beat with an electric mixer on medium-high speed until smooth.