Preheat oven to 350 degrees. Coat 2-quart baking dish with cooking spray. Toss potatoes, carrots and shallot with 1/4 cup melted butter, 1/4 cup brown sugar, 1/4 t. cinnamon, 1/8 t. nutmeg, salt and pepper.
Transfer to baking dish; cover. Bake 40 minutes or until potatoes and carrots are tender.
Meanwhile, mix flour, pecans, remaining brown sugar, cinnamon and nutmeg; stir in vanilla and remaining butter until crumbly. Top vegetables with crumb mixture. Bake, uncovered, 15-20 minutes or until lightly browned.