Bring a large pot of salted water to a boil and cook pasta according to package directions until al dente. Reserve 1 cup of pasta water before draining.
While pasta cooks, heat olive oil in a large skillet over medium heat. Add onions and sauté for 3-4 minutes until translucent.
Add minced garlic to the skillet and cook for another 30 seconds until fragrant, being careful not to let it brown or burn.
Stir in the pumpkin puree and broth, whisking to combine until smooth. Bring mixture to a gentle simmer.
Reduce heat to medium-low and add the cream, stirring continuously to incorporate. Let the sauce simmer gently for 2-3 minutes to thicken slightly.
Crumble in ⅔ of the feta cheese (reserving some for garnish) and stir until it begins to melt and incorporate into the sauce.
Add the sage and nutmeg, stirring to distribute the flavors evenly throughout the sauce.
Season with salt, pepper, and red pepper flakes if using. Taste and adjust seasonings as needed.
Add the drained pasta directly to the sauce, tossing to coat. If the sauce seems too thick, add some of the reserved pasta water, a little at a time, until you reach your desired consistency.
Serve immediately in warm bowls, topped with the remaining feta, fresh black pepper, and toasted pine nuts or pumpkin seeds if using.