Preheat oven to 375 degrees. Lightly oil a 13 X 9 inch non-stick casserole dish.

Remove stem and blossom ends of zucchini and cut crosswise into 1/4 inch thick slices. Trim and peel eggplant and cut crosswise into 1/2 inch thick slices. Remove core and seeds from bell pepper and cut into 1/4 inch thick rings. Peel onions and cut into thin slices. Layer the vegetables in prepared casserole dish, alternating with basil and thyme.

Heat oil in a small pan over medium-low heat. Add the minced garlic and shallot and cook, stirring constantly, 1 minute, or until shallot and garlic begin to soften. Stir the tomato juice, salt and pepper into the pan. Spoon tomato juice mixture over the vegetables in the casserole dish.

Bake the casserole 35-40 minutes, or until the vegetables are firm-tender. Combine cheeses with parsley and sprinkle over the casserole. Bake 10-15 minutes, or until the cheeses are melted and the vegetables are tender.