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Preheat oven to 350°F. Whisk together flour, cinnamon, pumpkin pie spice, baking soda, and salt in a large bowl; set aside. Beat sugars, oil, and pumpkin with an electric mixer on medium speed until well combined, about 1 minute. Beat in eggs one at time, beating well after each addition; stir in vanilla. Gradually beat in flour mixture on low speed until just combined.
Transfer mixture to a large piping bag or zip-top plastic bag fitted with a medium round tip. Pipe batter in 2-inch circles 2 inches apart on 2 parchment-lined baking sheets.
Bake in preheated oven 11 minutes or until tops are set, rotating baking sheets halfway through baking time. Let cool on baking sheets 5 minutes, then transfer to a wire rack to cool completely, about 30 minutes.
Beat cream cheese and butter with an electric mixer on medium speed until smooth. Gradually beat in powdered sugar on low speed until smooth, about 1 minute. Stir in vanilla and cinnamon.
Place frosting in a large piping bag or zip-top bag fitted with a medium round tip. Pipe frosting onto the flat side of half of the cookies. Top frosting with another cookie to create whoopie pies. Serve immediately, or chill overnight. Store in the refrigerator up to 4 days.