Preheat oven to 375F. In a large oven safe skillet*, heat oil over medium heat. Once hot, add the onions, peppers, and garlic. Saute until softened, about 3-4 minutes.
Add tomato paste and tomatoes. Stir together. Add seasonings (dried basil to red pepper flakes), balsamic and brown sugar. Stir together until well combined. Remove from heat.
Take a tomato, zucchini, squash, eggplant, and onion slice and make a stack. Place on the outer edge in the skillet sideways on top of the sauce. Working from the outside to the center of the skillet, repeat until all the vegetables are used up. Cover with oven safe lid, foil or something like a pizza stone. Bake for 35-40 minutes. Uncover, and cook for an additional 20 minutes.
While baking, to a small bowl add all the ingredients for the garlic butter together and stir. When ratatouille if finished, brush the butter on top. Top with fresh parsley, thyme, and/or basil.
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Notes
*Nutritional Facts are only estimates. Please utilize your own brands for accuracy. *If you do not have an oven safe skillet, cook sauce in a pot and then transfer to an oven safe dish, like a 9x13 casserole dish.*For an easier alternative (with taste changes) - you can use a jarred spaghetti sauce for the sauce (you will need 84-96oz) and cube your vegetables instead of thinly slicing. * To slice easier - use a mandolin with cut-resistant gloves. *Sometimes thin eggplants are mislabeled in stores. There is a slight taste difference between true Chinese and Japanese eggplant. What you are looking for is slender eggplant, dark in color, that is a similar size to a small zucchini.