Set an oven rack to the middle of the oven. Heat the oven to 350°F.
Make the crumble: In a medium bowl, combine the flour, brown sugar, and cinnamon. Add the butter and work it in with your fingertips until you have a uniform, moist crumble. Cover with plastic wrap.
Make the muffins: Butter and flour 12 regular (1/2-cup) or 6 large (1-cup) muffin tins or line them with paper liners. In a small bowl, sift together both flours, the baking soda, baking powder, salt, cinnamon, and nutmeg. Using a hand mixer or stand mixer fitted with the paddle, cream the butter and sugar in a large bowl until light and fluffy, about 3 minutes. Add the eggs, one at a time, beating well after each addition. Scrape the sides of the bowl and beat in the vanilla. On low speed, add the flour mixture in three additions, alternating with the buttermilk in two additions, beginning and ending with the flour. Gently fold in the berries by hand. Spoon the batter into the muffin cups to almost full.
Scatter a generous amount of the crumble over the batter in each muffin cup (there may be some leftover).
Bake until the tops are golden and spring back when touched lightly and a wooden skewer inserted in the center comes out clean, 20 to 25 minutes for regular muffins, 30 to 35 minutes for large. Cool in the pan for 5 minutes and then turn out onto a rack. Serve warm (slathered with butter if you like) or at room temperature.