In a large bowl, mix together all-purpose flour (1 ⅔ cups), granulated sugar (1 ½ cups), baking soda (1 teaspoon), baking powder (½ teaspoon), cinnamon (1 teaspoon), salt (½ teaspoon), and nutmeg (¼ teaspoon) together with a whisk.
Stirring between each addition, add eggs (2 large), canned pumpkin (15 ounces), vegetable oil (½ cup), and water (¼ cup) and continue mixing with a spatula or wooden spoon until ingredients are incorporated and you can no longer see the flour. To avoid overmixing, I suggest mixing this by hand with a spatula. If you are using an electric mixer, be sure to use the lowest speed setting and stop mixing as soon as flour disappears.
Scoop 3 tablespoons of batter in each cupcake liner and gently shake pan to even out the batter. Bake at 350℉ for 18-22 minutes, or until toothpick comes out clean. Cool completely before frosting.
How to Make Cream Cheese Frosting
Using a stand or hand-held mixer, beat the cream cheese(8 ounces) for 1-2 minutes until smooth and creamy. Scrape down the sides with a spatula, as needed.
Add softened unsalted butter (½ cup, i.e., 1 stick) and vanilla extract (1 ½ teaspoons) and continue mixing for 1 minute until combined. Lastly, slowly add in powdered sugar (2 cups) and a pinch of salt then beat on high speed for 30 seconds until well combined.
Use a knife or piping bag to frost the cooled cupcakes. This recipe will lightly frost roughly 24 cupcakes (if spreading on with a knife). Because this frosting is on the creamy side, it's best spread vs. trying to pipe on intricate swirls with a piping tip.