Preheat the oven to 450 degrees.
Place red peppers on a baking sheet, drizzle with one tablespoon olive oil and bake for 30 to 40 minutes, until skins are charred, turning twice during roasting. Remove from the oven and immediately cover tightly with aluminum foil. Let peppers sit for 30 minutes. Remove stem and cut in quarters. Remove the skins and seeds and cut into 1/2 inch strips. Set aside.
Lower oven to 375 degrees. Brush a round baking dish (I used a 10 inch baking dish) with olive oil. Set aside.
Add 2 tablespoons olive oil to a large skillet over medium high heat. Add onions and season with salt and pepper. Cook until translucent and softened, about 5 minutes. Add garlic and continue to cook for 1-2 minutes. Spread mixture in bottom of prepared dish.
In a large bowl, combine sliced eggplant, zucchini and tomatoes. Toss with the remaining 2 tablespoons olive oil, salt, pepper and one tablespoon thyme leaves.
Arrange the vegetables in a overlapping pattern (as pictured) alternating eggplant, zucchini, tomatoes and roasted red pepper. Drizzle oil left in bowl over vegetables. Sprinkle with remaining one tablespoon thyme leaves and capers. Cover tightly with foil and bake for 45 minutes.
Remove foil and sprinkle evenly with panko and parmesan cheese. Return to oven and bake uncovered for an additional 25 minutes until lightly browned. Serve warm.