In a large bowl, combine sliced zucchinis, cherry tomatoes, red bell pepper, onion, and minced garlic. Drizzle with olive oil, and season with oregano, basil, crushed red pepper flakes, salt, and pepper. Toss to coat the vegetables evenly.
In a baking dish, lay the chicken breasts flat and season them with salt and pepper on both sides. Arrange the vegetable mixture evenly around the chicken in the baking dish.
Sprinkle the shredded mozzarella cheese evenly over the vegetables and chicken, followed by the grated Parmesan cheese.
Cover the baking dish with aluminum foil and bake in the preheated oven for 25 minutes.
After 25 minutes, remove the foil and bake for an additional 15 minutes or until the chicken is cooked through and the cheese is bubbly and golden.
Let the dish rest for 5 minutes before serving. Garnish with fresh basil leaves if desired.