Preheat oven to 375°F and lightly grease a large oven-safe skillet or baking dish.
Spread crushed tomatoes evenly across the bottom of the pan, then sprinkle with diced onion, minced garlic, half the basil, salt, and pepper.
Arrange the sliced vegetables in alternating patterns in a circular spiral or rows on top of the tomato mixture, standing them slightly upright and overlapping.
Drizzle the arranged vegetables with olive oil and sprinkle with remaining basil, thyme, salt, and pepper.
Cover the pan tightly with foil and bake for 40 minutes until vegetables are tender.
Remove foil, sprinkle with Parmesan cheese, and bake uncovered for an additional 10 minutes until lightly golden.
Let rest for 5 minutes before serving with crusty bread.