Preheat your oven to 350°F (175°C). Grease a 2-quart baking dish with cooking spray or butter.
In a large pot, bring water to a boil. Add the sliced squash and chopped onion, and cook for about 5 minutes until tender. Drain and let cool slightly.
In a large mixing bowl, combine the cooked squash and onion with the shredded cheddar cheese, crushed crackers, milk, eggs, melted butter, salt, black pepper, garlic powder, onion powder, and paprika. Mix well until all ingredients are evenly incorporated.
Pour the mixture into the prepared baking dish and spread it evenly.
Bake in the preheated oven for 30-35 minutes, or until the top is golden brown and the casserole is set.
Remove from the oven and let it cool for about 5 minutes before serving.