Heat the oven to 400 degrees F. Put a half sheet pan in the oven to heat for 15 minutes.
Trim the woody ends and halve the squash crosswise. Scoop out the squash seeds, leaving a 1/2-inch shell. Reserve the flesh. Brush the cut sides of the squash with 1 tablespoon of the olive oil, and season with 1/2 teaspoon of salt and 1/4 teaspoon of pepper. Arrange the squash, cut side down, onto the preheated pan and roast until the squash is tender and the flesh side is browned, about 15 minutes. Transfer the squash to a serving platter and set aside.
Meanwhile, finely chop the reserved squash flesh. Heat a 10-inch cast iron skillet over medium heat and add the remaining tablespoon of olive oil. When the oil shimmers add the chopped squash, shallot, garlic, remaining 1/2 teaspoon salt, and 1/4 teaspoon of pepper. Cook, stirring occasionally, until tender and browned, about 2 to 3 minutes. Add the corn, limas, pecans, and thyme. Cook until heated through, approximately 1 minute. Divide the stuffing evenly among the cooked squash and serve immediately.