To keep pancakes warm while you are making the whole batch, heat oven to 200°F and place a large sheet pan inside.
In a large bowl, mix 2 cups all-purpose flour, 2 tablespoons sugar, 2 teaspoon baking powder, 1 teaspoon baking soda, 1/2 teaspoon salt, and 1/4 teaspoon ground nutmeg or cinnamon (if using).
Add the 2 large eggs lightly beaten, 2 cups buttermilk *see note, and 1 teaspoon vanilla extract and whisk until just combined. Some small lumps remaining are fine. (Do not over stir the mixture. Overmixing makes for a flat pancake. Mix until a few streaks of flour are remaining.) Let batter sit for about 10 minutes.
While the batter rests, make the cinnamon swirl mixture. In a small bowl, stir together the 2/3 cup packed brown sugar, 5 tablespoons melted unsalted butter, and 1 tablespoon ground cinnamon until smooth. Transfer the mixture to a quart-size zip-top bag and set aside.
Preheat a large skillet or griddle over medium-high heat. It should be hot before adding the pancakes to the surface. Spray surface with cooking spray or grease with a bit of oil or melted butter. When pan is hot and right before cooking the pancakes, lower the heat to medium and spoon out 1/3 cup of batter for each pancake.
When the pancakes begin to form bubbles, snip the tip of the cinnamon filling bag to make a very small hole in the corner, and squeeze the cinnamon in a spiral swirl on top of the pancake. Start from the center and make a swirl going outward.
Cook each pancake for about 2-3 minutes. If pancakes are browning too quickly, lower the heat. Bubbles will form on the edges of the pancakes and once they look dry, use a thin spatula to gently lift one side and take a look underneath. If the pancake is golden, flip and cook on the other side for about 2 1/2 minutes, or until golden brown.
While the pancakes are cooking, make the cream cheese glaze. Add the 4 tablespoons unsalted butter and 2 ounces cream cheese to a microwave-safe bowl. Heat for 30 seconds, then stir. Continue microwaving in 15-second bursts, mixing after each, until fully melted. Stir in the 3/4 cup powdered sugar and 1/2 teaspoon vanilla extract, then set aside.
Remove pancakes and either serve immediately or keep warm in the oven. Wipe the pan, if needed, and spray or grease surface again and continue cooking remaining batter.
To serve, stack a couple of pancakes on a plate and top with the cream cheese glaze.