Step 1Heat the oven to 375 degrees.
Step 2Cut the squashes in half crosswise and scoop out the seeds. Trim about one-fourth inch off the bottom of each so it will stand up. Place cut side up on a baking sheet. Season with salt and pepper to taste and dot with 1 tablespoon of the butter. Bake until very tender, about 1 hour.
Step 3Meanwhile, heat the oil in a large skillet over medium heat. Add the pancetta and cook until browned and crisp, 5 minutes. Add the onion and cook, stirring frequently, until softened, about 4 minutes. Add the brown rice, wild rice, pine nuts, dried cranberries, thyme and lemon juice. Stir to combine. Set aside.
Step 4Remove the squash from the oven and carefully scoop out the cooked squash; keep the shells intact. Chop the cooked squash and stir into the rice. Adjust the salt and pepper. Spoon the rice into the squash shells and set them on a baking sheet. Top each with a small piece of the remaining butter. Bake until the rice is heated through and the tops are slightly crisp, 30 to 40 minutes.