Preheat the oven to 450 degrees F. Wash the outside of the squash. Cut the squash in half lengthwise and scoop out the seeds (I use an ice cream scoop). Place the squash halves cut-side up in a large baking dish. Sprinkle the surface of the squash with salt and pepper. Pour 1/4 inch of water in the bottom of the pan and cover the pan tightly with foil. Bake the squash until it is tender when pierced with a fork, 30-50 minutes depending on the size (my little ones were done in 30). Remove from the oven, discard foil, and allow the squash to cool.
Reduce oven temperature to 400 degrees F.
Meanwhile, cook the quinoa by bringing 1 and 1/3 cup water to boil in a small pot. Add the quinoa, reduce to a simmer and put a lid on the pot. Simmer for 15 minutes. Remove the pan from the heat.
Heat a skillet over medium heat. Toast the pecans until fragrant, about 5 minutes. Set aside. In the same skillet over medium heat, combine the olive oil and shallots. Cook, stirring frequently, until the shallots soften, about 5 minutes. Remove the skillet from the heat.
Using a spoon or an ice cream scoop, gently scrape the flesh out of the roasted squash halves, leaving a layer of about 1/4 inch of squash remaining in the shell. (Leave the squash shells in the baking dish.) In a large bowl combine the squash, cooked quinoa, pecans, shallot, oregano, and salt. In another small bowl whisk together the panko breadcrumbs and butter.
Finely grate the parmesan cheese. Add 2 Tbsp. of the cheese to the panko. Add the remaining parmesan to the squash mixture and stir to combine all of the ingredients.
Gently spoon the squash mixture into the squash shells. Sprinkle the panko and parmesan over the top.
Return squash to the oven and bake, uncovered, until the tops are golden brown, 20-25 minutes.