Preheat oven to 350. Line a muffin tin with muffin cups.
In a medium bowl, combine flours, baking powder, pumpkin pie spice, salt and 1 TSP of the cinnamon.
In another bowl, beat butter, Greek yogurt, 1 cup of the pumpkin, 1 cup of the brown sugar, and 1 TSP of the vanilla extract with an electric mixer until smooth.
Slowly mix the wet mixture in with the dry mixture, and stir just until combined.
Pour batter evenly into muffin cups.
Bake for about 25 minutes, or until golden brown and a toothpick can puncture muffins and come out clean.
Once muffins are done cooking, remove from oven and place on a wire rack to cool.
Meanwhile, combine the cream cheese, remaining pumpkin (1/2 cup), vanilla extract (1 TSP), brown sugar (1/2 cup), and cinnamon (1 TSP) in a bowl. Beat until smooth.
Allow the muffins to completely cool, then use a butter knife to spread the cream cheese frosting on top of each one.
Dress them up with toppings of your choice, or eat them plain in all their pumpkin-flavored glory.