Heat the oil in a large skillet over medium heat. Add the onions and cook until translucent, about 3 minutes. Add the garlic and cook until fragrant, about 1 minute. Add the wine. Increase the heat to high and boil the wine until almost evaporated, about 3 minutes. Add the tomatoes and chile flakes and bring the sauce to a boil. Cook, about 10 minutes. Add the flounder, shrimp and capers. Sprinkle with salt and pepper. Simmer the mixture until the flounder and shrimp are almost cooked through, about 1 1/2 minutes.
Meanwhile, boil a pot of salted water. Cook the pasta until tender but still firm to bite, about 8 minutes.
Ladle out 1/4 cup pasta cooking water and reserve. Drain the pasta. Add the pasta and reserved water to the skillet and toss gently. Cook on low, about 2 minutes. Sprinkle with salt and pepper. Transfer the pasta to a bowl and serve with the Parmesan if desired.