Preheat your oven to 375°F. In a 10-inch oval oven-safe baking dish, mix together the chopped onions, minced garlic, diced tomatoes, fresh thyme, ¼ teaspoon of salt, ¼ teaspoon of black pepper, and crushed red pepper.

Start at the outer edge of the dish and layer alternating slices of eggplant, zucchini, yellow squash, and red bell pepper. Overlap the slices slightly to showcase their colors and create a pleasing pattern.

Drizzle the layered vegetables with olive oil and season with oregano, and the remaining salt and pepper. Cover the dish with aluminum foil and bake for 45 minutes.

Remove the foil and continue baking for another 15 minutes or until the vegetables become tender. Drizzle with red wine vinegar and sprinkle Parmesan cheese on top, if desired.