Heat a large Dutch oven or skillet over medium heat. Add the olive oil. Season the chicken pieces with salt and pepper. Add half the chicken and cook, skin side down, until crisp and browned. Turn the pieces over and cook another 5 minutes. Remove to a plate and continue browning in small batches until all chicken is browned. Reserve 1 tablespoon of the drippings in the pan.
Add the onions, mushrooms and a pinch of salt to the pan with the reserved drippings. Cook over medium-high heat until the vegetables begin to brown and the moisture evaporates.
Add the garlic and red pepper flakes to the pan and sauté until fragrant, about 30 seconds. Stir in the flour and continuing cooking and stirring for 1 more minute. Add the wine, tomatoes, tomato paste, bay leaves, Parmesan rind, thyme, oregano and red bell pepper.
Remove the skin from the chicken and discard. Add the skinless chicken pieces to the pan, pressing them down into the sauce so they are covered. Bring to a boil, cover and reduce the heat to low. Simmer until the chicken is tender, about 40-45 minutes. Halfway through cooking, move the chicken pieces around and/or turn them over to ensure even cooking.
Remove the bay leaves and Parmesan rind and discard. Check seasoning and add salt and pepper if needed. Garnish with fresh chopped parsley leaves. Serve over hot cooked spaghetti or polenta.