Preheat oven to 350 degrees F (175 degrees C)
Arrange the squash halves cut side up in a baking dish
Fill dish with about 1/4 inch water
Place 1 tablespoon butter on each half, and season halves with salt and pepper
Cover dish, and bake squash 30 minutes in the preheated oven, or until very tender
Place quinoa in a pot with 2 cups water
Bring to a boil
Reduce heat to low, cover, and simmer 15 minutes
Melt the remaining 1 tablespoon butter in a skillet over medium heat
Stir in shallots and garlic, and cook until tender
Stir in pine nuts, and cook until golden
Gently mix into the pot with the cooked quinoa
Cut the squash halves in half, and fill each quarter with the quinoa mixture
Serve each stuffed squash quarter on a bed of the remaining quinoa mixture