Preheat oven to 350 degrees. Line a standard muffin pan with paper liners. In a medium bowl, whisk together flour, sugar, baking powder, baking soda, and salt.
Make a well in the center of flour mixture. In well, mix together butter, applesauce, mashed bananas, eggs, and vanilla. Stir to incorporate flour mixture (do not overmix). Dividing evenly, spoon batter into muffin cups.
Bake until a toothpick inserted in center of a cupcake comes out clean, about 25 minutes. Remove cupcakes from pan; cool completely on wire rack. Spread tops with Honey Cinnamon Cream Cheese Frosting.
For the Frosting:
Cream butter until light and fluffy. Add the cream cheese and beat for another 2 minutes.
Add the honey and cinnamon, and gradually add the powdered sugar one cup at a time.
Add the milk and more powdered sugar (if needed) until you get your desired consistency.