Heat oven to 350°F. Line a 12-cup muffin pan with paper liners. In a large bowl, whisk together flours, sugar, baking soda, cinnamon, and salt. In a second bowl, whisk together eggs, oil, and vanilla. Stir in pineapple, bananas, and pecans. Fold into flour mixture until just combined.
Divide evenly among the liners (about 5 Tbsp each) and bake until a wooden pick inserted into center comes out clean, 27 to 30 minutes. Let cool in pan 10 minutes, then transfer to wire rack to cool completely.
FROSTING
In a food processor, pulse dried pineapple to make fine powder. Pass through a fine-mesh sieve.
Using an electric mixer, beat cream cheese and butter on low speed until smooth. Add sugar and beat on low speed to combine. Mix in pineapple powder and vanilla. Cover and refrigerate until thickened, about 1 hour. Spread each cupcake with frosting.
FLOWER PETALS
Cut pineapple into 1/4-inch-thick rings; cut each ring into 8 wedges. Create a flower on each cupcake by placing a blueberry in the center and surrounding with 4 pineapple petals.