Preheat oven to 325°. In small bowl, combine 1/4 cup melted butter, brown sugar and maple syrup. Divide between 12 greased jumbo muffin cups. Sprinkle with pecans; set aside.
In a large bowl, beat cream cheese, sugar and vanilla until smooth. Add eggs, 1 at a time until blended. Remove 1 cup for filling. Stir in pumpkin, flour and pie spice to remaining cream cheese mixture; set aside.
Place one sheet of phyllo dough on a work surface; brush with butter. Layer with 5 additional phyllo sheets, brushing each layer. (Keep remaining phyllo covered with plastic wrap and a damp towel to prevent it from drying out.) Cut sheets into a 9×7-in. rectangle. Carefully press each stack into prepared muffin cups. Repeat with remaining phyllo.
Spoon 1 heaping tablespoon plain cream cheese mixture into each phyllo cup. Top with 3 tablespoons pumpkin mixture. Pinch corners of phyllo together and twist to seal; brush with remaining butter. Bake until golden brown, 45-50 minutes. Cool 5 minutes before inverting onto wire racks to cool completely. If desired, serve with whipped cream and sprinkle with additional pumpkin pie spice.