Heat 1/2 cup olive oil in a medium (10 to 11-inch) pot or Dutch oven, such as Le Creuset, over medium heat. Add the eggplant and saute for 5 minutes, stirring frequently, until tender. Add a little more olive oil if the eggplant is sticking.
Add 2 tablespoons olive oil to the pot, add the onions and fennel, and cook for 6 to 8 minutes, stirring occasionally, until the onion is tender but not browned. Add the garlic and cook for one minute, stirring often. Add the chicken stock, crushed tomatoes, fennel seeds, oregano, thyme, red pepper flakes, 1 tablespoon salt, and 2 teaspoons black pepper. Pour the can of whole tomatoes, including the liquid, into a food processor and pulse until the tomatoes are coarsely chopped. Add the tomatoes and the liquid to the pot. Bring to a boil, lower the heat, and simmer uncovered for 15 minutes, stirring occasionally. Taste for seasonings. Serve hot in large bowls sprinkled with Parmesan cheese and a drizzle of olive oil.