Preheat oven to 350°F (175°C). Line a cupcake pan with cupcake liners and set aside.
In a large skillet, melt 2 tablespoons of butter and stir in pecans. Toast over medium heat for about 4-5 minutes, watching carefully to prevent burning.
In the bowl of an electric mixer, cream together the remaining butter (1 cup) and granulated sugar until light and fluffy.
Add eggs, one at a time, beating well after each addition. Beat in vanilla extract.
In a separate mixing bowl, combine all-purpose flour, cake flour, baking powder, salt, and cinnamon.
Add the dry ingredients to the mixer, alternating with milk, beginning and ending with the dry ingredients.
Fold in the toasted pecans with a spoon. Fill cupcake liners 2/3 full and bake for 21-23 minutes or until a toothpick inserted in the center comes out clean. Allow cupcakes to cool completely before frosting.
For the frosting, using an electric mixer, cream together cream cheese and butter until light and fluffy.
Add in brown sugar and cinnamon, and continue to cream together for 3-4 minutes.
Gradually add powdered sugar, 1 cup at a time, until desired consistency is reached. For a thicker frosting, add additional powdered sugar.
Pipe frosting onto cooled cupcakes and top with additional toasted pecans or candied pecans if desired.