Prepare phyllo cups according to directions on package. While cooling, prepare rest of ingredients.
Evenly spread pecan chips on a baking sheet. Toast for 7 minutes in 350° Fahrenheit oven. Pecans should be brown and fragrant. Set aside to cool.
In a small mixing bowl, mix together pumpkin, pudding mix, whipped topping and pumpkin pie spice using a hand mixer or by hand. Spoon pumpkin filling into a piping bag or piping gun with large plain tip and set aside.
In another small bowl, mix together ingredients for the cream cheese topping. When well blended, spoon this topping into 2nd piping bag or piping gun with a large star tip.
Pipe pumpkin filling into all of the phyllo cups, filling the cups almost to the top. Top with cream cheese topping. Sprinkle with pecan chips and cinnamon to serve!