In a large skillet, melt butter over medium heat and sauté the chopped onion until translucent.
Add the onions, shredded carrots, and broccoli florets into the slow cooker.
Pour in the chicken broth and season with garlic powder, onion powder, nutmeg, pepper, and salt.
Cover and cook on low for 4-6 hours or on high for 2-3 hours, until the vegetables are tender.
In a small bowl, whisk together the heavy cream and flour until smooth. Stir into the soup and let it cook for another 30 minutes on high until thickened.
Stir in the cheddar and mozzarella cheese until melted and creamy.
Serve warm with crusty bread or a fresh salad.