Bring a saucepan of water to a boil. Plunge tomatoes into the boiling water and immediately remove to a medium bowl of ice water; drain. Remove and discard skins from tomatoes. Chop tomatoes and set aside.
Heat olive oil in a skillet over medium heat; saute onion until tender, about 5 minutes. Stir in tomatoes, garlic and Italian seasoning; cook until tomatoes are tender, 5 to 7 minutes. Mix in olives, wine, capers, lemon juice, and 1/2 the basil. Reduce heat, blend in Parmesan cheese, and cook until the mixture is reduced to a thick sauce, about 15 minutes.
Place flounder in a shallow baking dish. Pour sauce over the fillets and top with remaining basil leaves.
Bake 12 minutes in the preheated oven, until fish is easily flaked with a fork.