Preheat your oven to 375°F (190°C).
Heat 2 tablespoons of olive oil in a large skillet over medium heat. Add the chopped onion and garlic, sautéing until translucent and fragrant, about 3-4 minutes.
Stir in the diced tomatoes, thyme, rosemary, basil, salt, and pepper. Reduce the heat and let the mixture simmer for 10 minutes, allowing the flavors to meld.
While the tomato sauce simmers, arrange the sliced zucchini, yellow squash, eggplant, and bell peppers in a circular pattern in a greased 9-inch (23cm) baking dish, alternating and overlapping them as needed.
Once the sauce has thickened, taste and adjust the seasoning if necessary. Pour the sauce evenly over the arranged vegetables.
Drizzle the remaining olive oil over the top and cover the dish with aluminum foil.
Bake in the preheated oven for 30 minutes. After 30 minutes, remove the foil and bake for an additional 10 minutes or until the vegetables are tender and slightly caramelized.
Remove from the oven and let it rest for 5 minutes before serving. Garnish with fresh basil leaves if desired.