Divide the oil over the 4 squash halves and use your fingers or a brush to spread the oil over the squash flesh. Bake cut side facing down on a baking pan for 25 - 35 minutes until the squash is fork-tender.
To make the quinoa filling:
Heat the oil in a large high sided pan or pot over medium-high heat. When hot add the onions and garlic and sauté until the onions turn translucent and just begin to brown, about 5 minutes. Add the quinoa and vegetable broth and cover with a lid. Bring to a simmer and continue to simmer for 10 - 15 minutes until the vegetable broth is absorbed and the quinoa is cooked.
Once the quinoa is cooked, stir in all of the remaining ingredients, the nuts or seeds, cranberries, thyme, sage, pepper, cinnamon, and add salt to taste. I found the vegetable broth I used had enough salt so I did not need extra, but taste your dish and add more if needed. Remove from heat.
To stuff the acorn squash:
Divide the quinoa mixture evenly among the acorn squash halves, packing it into the well of the squash. You may have extra quinoa leftover. Serve hot, and garnish with more fresh thyme or sage as desired. See notes for making this dish ahead of time.
For oil-free: omit oil on squash and instead line the baking sheet with parchment paper. When preparing the quinoa, sauté the vegetables in water or broth instead of oil.To use dried spices: replace fresh sage with ¼ teaspoon dried sage, and replace fresh thyme with ½ teaspoon dried thyme leaves. Note that the stuffing won't have pretty green specks in it.To make ahead: you can prepare the entire dish ahead of time. Allow the squash and quinoa to cool completely before covering and storing in the fridge for up to 2 days. To reheat, cover in foil in an oven preheated to 400F (200C) until heated through. If you like you can remove the foil for the last 5 - 10 minutes to crisp up the top slightly.