Cook the manicotti shells according to package directions, stopping when they are just al dente. Drain and set aside to cool slightly.
Preheat oven to 375°F. Lightly grease a 9x13-inch baking dish.
In a large bowl, combine the pumpkin puree, drained ricotta, egg, Parmesan, kosher salt, garlic powder, onion powder, black pepper, basil, parsley, nutmeg, cinnamon, and maple syrup. Stir until smooth and evenly combined.
Add the butter to a medium saucepan over medium heat. Cook until melted and foamy. Continue cooking, swirling the pan occasionally, until the milk solids turn golden brown and the butter smells nutty and fragrant.
Add the chopped sage and cook for 30–60 seconds, until fragrant. Remove some of the fried sage and set aside for topping later.
Reduce the heat to medium-low and whisk in the flour. Cook for about 1 minute, whisking constantly.
Slowly whisk in the heavy cream until smooth. Cook for 3–5 minutes, stirring frequently, until the sauce has slightly thickened.
Remove the saucepan from the heat. Whisk in the Parmesan until smooth and creamy. Season with black pepper and a pinch of kosher salt. Taste and adjust seasoning as needed.
Spread a thin layer of the brown butter sage cream sauce across the bottom of the prepared baking dish.
Transfer the pumpkin ricotta filling to a piping bag or large zip-top bag with one corner snipped off. Carefully pipe the filling into each manicotti shell. You can also use a small spoon if preferred.
Place the filled manicotti in a single layer in the prepared baking dish.
Pour the remaining brown butter sage cream sauce evenly over the manicotti, making sure the pasta is well covered.
Sprinkle the Gruyère evenly over the top.
Loosely cover the baking dish with foil and bake for 20 minutes.
Remove the foil and continue baking for 8–10 minutes, until the cheese is melted and bubbling and the edges are lightly golden.
Optional: For a deeper golden-brown topping, broil for 1–2 minutes, watching closely so the cheese doesn't burn.
Let the manicotti rest for 5–10 minutes before serving. Garnish with freshly grated Parmesan, freshly cracked black pepper, and crispy sage leaves if desired.