Heat oven to 425°F. On rimmed baking sheet, toss onions, squash and fennel with 1 tablespoon oil, thyme and ¼ teaspoon each salt and pepper; roast 15 minutes.
Meanwhile, heat remaining 2 teaspoons oil in medium skillet on medium. Season chicken with ¼ teaspoon each salt and pepper and cook, skin side down, until deep golden brown, 8 to 10 minutes. Flip and cook 3 minutes more.
Nestle chicken among veggies and roast until chicken is cooked through, 15 to 18 minutes. Transfer chicken to cutting board; let rest at least 5 minutes.
Meanwhile, continue roasting vegetables until ready to serve, about 5 minutes. Slice half of chicken and serve with one-third of vegetables. Refrigerate leftover chicken and vegetables for lunch the next day.
