In a skillet over medium heat, add olive oil. Sauté the chopped onion for 5 minutes until translucent. Add minced garlic and cook for another minute.
In a large bowl, mix the zucchini, yellow squash, sautéed onions and garlic, Greek yogurt, Italian seasoning, and half of the cheddar cheese. Season lightly with salt and black pepper.
Lightly grease a casserole dish with cooking spray. Spread the vegetable mixture evenly in the dish.
In a small bowl, combine the breadcrumbs and Parmesan cheese. Sprinkle the remaining cheddar cheese over the casserole, then top with the breadcrumb mixture.