Spaghetti Squash with Pine Nuts and Sage

1 medium (2 pound) spaghetti squash
2 teaspoons olive oil
1 onion, minced
1 large shallot, minced
2 garlic cloves, minced
1/4 cup pine nuts
2 tablespoons freshly grate Romano cheese
1 tablespoon minced fresh sage
1/4 teaspoon crushed red pepper flakes
sea salt, to taste
freshly ground pepper, to taste

Preheat oven to 400 degrees F. Place the squash halves cut side down on a parchment paper-lined baking sheet and roast for about 50 minutes, or until tender.
Meanwhile, heat the olive oil in a skillet over medium heat. Add the onion, shallot, and garlic and sauté for 4 minutes. Add in the pine nuts and cook for 2 minutes until the pine nuts are lightly browned. Set aside.
When the squash is cooked, turn over squash to cut side up. With a pasta rake or large spoon, scoop the flesh from the squash shell. The flesh will come out like strands of spaghetti. Add the squash to a large serving bowl and rake through the strands to keep them separated. Add in the pine nut mixture, cheese, sage, crushed red pepper flakes, salt, and pepper. Toss well and serve.