Preheat your oven to 375 degrees F. Butter an 8 by 8-inch casserole dish.
In a large heavy bottomed saute pan over medium heat, melt butter. Saute onion and garlic until translucent. Add zucchini and tomatoes, about 7 minutes Add thyme, and flour. Season with salt and pepper. Add mixture to the buttered casserole dish.
In a medium size bowl, add brown sugar, eggs, and half-and-half. Season with salt and pepper. Pour the milk mixture over the zucchini and sprinkle with both of the cheeses. Bake for 30 minutes.