Prepare the tomato sauce:
Heat 1 tablespoon of olive oil in a skillet over medium heat. Add the chopped onion and minced garlic, and sauté until softened.
Stir in the crushed tomatoes, oregano, thyme, salt, and black pepper. Simmer for 10 minutes, then spread the sauce evenly on the bottom of a baking dish.
Layer the vegetables:
Preheat your oven to 375°F (190°C).
Arrange the sliced zucchini, yellow squash, eggplant, tomatoes, and bell peppers in a circular pattern on top of the sauce, alternating the vegetables for a colorful presentation.
Season and drizzle:
Drizzle the remaining 2 tablespoons of olive oil over the vegetables. Sprinkle with a pinch of salt, pepper, and additional thyme or oregano if desired.
Bake:
Cover the dish with aluminum foil and bake for 35 minutes. Remove the foil and bake for an additional 15 minutes, or until the vegetables are tender and slightly caramelized on top.
Garnish and serve:
Remove from the oven and sprinkle with fresh basil before serving. Serve hot as a side dish, over rice, or with crusty bread for a complete meal.