(Note: toss all pecans in a couple of tablespoons of flour to assure they don’t sink in the dish.)
Preheat oven to 350 degrees F (175 degrees C). Grease a 9×13-inch baking dish.
Beat 1 cup white sugar, 1/2 cup butter, and 1 egg in a bowl until smooth. Add sour cream and vanilla extract; mix well. Stir nuts into dry mixture of 3 cups flour, baking soda, and baking powder. Add to cream mixture until mixture comes together in a sticky dough. Spread half the dough evenly into prepared baking dish.
Beat cream cheese, 1/2 cup white sugar, and 1 egg in another bowl until smooth. Spoon mixture into baking dish over dough. Drop remaining half of dough by spoonfuls over cream cheese mixture.
Mix pecans, brown sugar, 1/3 cup flour, and 1/3 cup butter in a bowl until mixture resembles a coarse crumble; sprinkle over dough.
Bake in the preheated oven until a toothpick inserted into the center comes out clean, about 45 minutes.