In a large bowl, whisk together 2 cups of flour, white sugar, dark brown sugar, baking powder, cinnamon, nutmeg, allspice, ginger, cloves, and salt.
In a medium bowl, combine the milk, eggs, vanilla, pumpkin puree, and vegetable oil. Stir until the mixture is uniform.
In a small bowl, combine the softened cream cheese, powdered sugar, and 1 tablespoon flour. Stir to blend the ingredients until they are smooth.
Combine the pumpkin mixture with the dry ingredients and stir until the muffin batter is just mixed.
Line a 12-cup muffin tin with muffin liners. Place a little more than ¼ cup of batter in each liner. Then place a small dollop of the cream cheese mixture in the center of each muffin, and sprinkle the chopped pepitas around the edges.
Bake the muffins for 17 to 20 minutes.
Remove the muffins from the oven and let them rest in the pan for 10 minutes before removing them from the pan to cool completely.