For the cranberry, orange and pecan sauce: Combine the cranberries, granulated sugar, cinnamon, allspice, nutmeg, cinnamon stick, orange zest and juice and 1/2 cup water in a medium pot. Bring to a boil over medium heat, then reduce to a simmer and cook until some cranberries burst but some still remain whole, 8 to 10 minutes. Cool completely, remove the cinnamon stick and stir in the pecans.
For the pancake batter: Mix the flour, brown sugar, baking powder and salt in a large bowl. Whisk together the milk, butter, vanilla and eggs in a separate bowl. Make a well in the middle of the dry ingredients and pour the milk mixture into the well. Gently whisk until combined, but do not overmix, as it will make your pancakes chewy. Let the batter rest for 20 minutes.
Meanwhile, chop 1 cup of the pecans and set the remaining 1/2 cup aside.
Heat a large nonstick or cast-iron skillet and coat with about 2 tablespoons butter. Add a scant 1/2 cup batter per pancake to your pan, leaving space between each. Sprinkle a handful of the chopped pecans in each. Cook until you see bubbles on the sides and in the center of the pancakes, 2 to 3 minutes, then flip and cook for an additional 2 to 3 minutes. Remove from the pan to a flat surface to cool a few minutes. Cook the rest of the pancakes in butter in batches.
Hold a pancake flat and use a paring knife to make a 1/2-inch horizontal cut in the top. Slip the knife in horizontally and move it back and forth while turning the pancake to make a pocket. Repeat with all the pancakes. Spoon some sauce inside each pocket. (See Cook's Note.) Make stacks of stuffed pancakes on a serving platter. Or, stuff a few and serve with the remaining sauce on the side. Top with the reserved pecan halves for garnish.
You can also pipe the filling in the pancakes using a resealable plastic bag with a corner cut off.