Cut eggplant in half lengthwise; remove pulp, leaving a 1/4-in.-thick shell. Cube pulp; set shells and pulp aside., In a large nonstick skillet coated with cooking spray, saute onion and garlic until onion is tender. Add the mushrooms, zucchini, red pepper and eggplant pulp; saute for 4-6 minutes or until vegetables are crisp-tender. Stir in the tomatoes, wheat germ, parsley, thyme, salt, pepper and pepper flakes; cook for 1 minute. , Divide mixture evenly between the eggplant shells; sprinkle with Parmesan cheese. Place on a baking sheet. Bake at 400° for 20-25 minutes or until shells are tender.