Preheat oven to 375 degrees. Place onions, garlic, and pepper in a glass baking dish, toss with olive oil. Bake 15 minutes, stir, bake 15 minutes more. Stir in fennel, tomatoes, oregano, chili; bake 15 minutes. Add wine, vinegar, and arrowroot; bake 25 minutes. Prepare pasta according to package instructions. Serve vegetables and sauce over pasta; sprinkle with cheese.