Pre-heat oven to 450 F degrees. Line a baking sheet with aluminum foil and set aside.
Place butternut squash in a large mixing bowl and toss with 1 tablespoon olive oil, 1 teaspoon salt, cinnamon, paprika and cayenne pepper (if using) until well coated. Pour out onto the prepared baking sheet in a single layer. Place in the middle rack of the preheated oven and roast until tender, about 20 minutes. Remove from oven and set aside.
In the meantime, combine the quinoa, water (or broth) and 1/2 teaspoon of salt in a medium pot. Bring to a simmer then reduce the heat to low. Cover and cook undisturbed until the water has evaporated and the quinoa is tender, about 15 minutes. Remove from heat and leave covered an additional 5 minutes then fluff with a fork.
In a large shallow skillet, heat the remaining tablespoon of olive oil over medium heat. Add the shallots and saute until they begin to soften, adjusting the heat so that they don't brown, about 3 to 4 minutes. Add the cooked quinoa and roasted butternut squash to the skillet. Toss in the arugula and continue to cook until it just begins to wilt, about 1 to 2 minutes. Remove from heat and season with salt and freshly ground pepper to taste. Top with chopped pecans and serve.