Preheat oven to 400°F and line a baking sheet with parchment paper. Toss diced butternut squash and Brussels sprouts with 2 tablespoons olive oil, fresh thyme, salt, and pepper until evenly coated. Spread in a single layer and roast for 20 minutes until edges start turning golden brown.

While vegetables roast, bring a large pot of salted water to a boil and cook pasta according to package directions until al dente. Drain pasta using a colander, reserving 2 tablespoons pasta water, then toss with either a drizzle of olive oil or the reserved pasta water to prevent sticking. Let cool to room temperature, about 10 minutes.

After initial 20 minutes of roasting, push vegetables to one side of baking sheet and add diced apples to the cleared space. Continue roasting for another 10-15 minutes until everything is fork-tender and caramelized. Check at 30 minutes total - squash should pierce easily with a fork, Brussels sprouts should have golden-brown edges, and apples should be tender but still hold their shape.

Make maple dijon vinaigrette by whisking together olive oil, balsamic vinegar, dijon mustard, maple syrup, minced garlic, salt, and pepper in a small bowl for about 1 minute until smooth and emulsified.

Once roasted vegetables have cooled for 5-10 minutes until just warm to the touch, combine pasta, roasted vegetables, room temperature goat cheese, and dried cranberries in a large bowl. Pour dressing over everything and toss gently until all ingredients are well coated.