Preheat oven to 400° F. Grease 8x12 baking dish or spray with nonstick cooking spray.
Thinly slice zucchini, yellow squash, and butternut squash, making squash pieces about the same shape for stacking in baking dish.
Finely dice shallots and mince garlic. Sauté both in skillet with olive oil until softened (about 5 minutes). Add thyme and combine.
Spread the softened onion, garlic and thyme in the bottom of the dish. Place the thinly sliced vegetables in the baking dish vertically, alternating squash.
Sprinkle generously with salt, add pepper to taste.
Cover dish with foil and bake for 30-45 minutes. Remove foil, top with cheese and make for another 15-20 minutes or until cheese is golden brown.
Remove from oven and serve.