1. Preheat oven to 350 degrees. Prepare 3 (9-inch) round cake pans with nonstick spray, then line the bottom of each pan with parchment paper, and cover the paper with nonstick.
2. Spread pecans out evenly into a single layer in a pan, then bake 6-8 minutes, or until toasted and fragrant, stirring halfway through to toast evenly.
3. In a large mixing bowl, whisk together flour, sugar, cinnamon, salt, baking soda, and nutmeg. Add eggs, oil, and vanilla, stirring until just moistened. Gently fold in the bananas, pineapple, and 1 cup of the toasted pecans - batter should be quite thick, like a banana bread batter. Pour batter evenly into prepared cake pans.
4. Bake cakes for 28-30 minutes. Cool in pans on a cooling rack about 10 minutes, then remove cakes from pans to cooling rack, and cool completely (about 30 minutes). Remove and discard parchment paper.
5. While cakes are cooling, prepare cream cheese frosting. In a large mixing bowl, beat cream cheese, softened butter, and vanilla extract until smooth. Add in powdered sugar gradually, beating on low until blended. Beat on medium for another 3 minutes, or until fluffy.
6. Place 1 cooled cake layer on a cake stand or serving plate. Top with one-fourth of cream cheese frosting. Repeat once, then top with remaining cake layer. Spread remaining frosting over top and sides of cake. Garnish with remaining pecans.