Preheat oven to 350 degrees F. Grease a large rectangular casserole dish with butter or non-stick spray and set aside.

In a heavy bottom skillet add in 2 tablespoons of butter on medium-low heat. Once butter is melted, add in diced onions and cook for 35-40 minutes or until onions are caramelized and golden. Stir the onions periodically. About 5-10 minutes before finish cooking, add half a cup of dry white wine and cook until most of the liquid has dissolved. 

Bring a large pot of boiling salted water to a rolling boil. Add in macaroni noodles and cook until al dente. Reserve 1-2 cups of pasta water before draining. This is usually 1-2 minutes less than the package instructions. Drain noodles with cold water and set aside.

In a large pot or dutch oven add 4 tablespoons of unsalted butter over medium high heat until melted. Begin to whisk in flour until creamy and thickened to create a roux for the sauce for 1-2 minutes. Slowly whisk in the milk. Bring mixture to a low simmer until it is thick enough to coat the back of a spoon. Whisk in pumpkin puree, garlic, nutmeg, black pepper and season with salt to taste. Stir in cheeses until melted. If mixture becomes very thick, add in ½ cup of pasta water at a time to loosen. Remove from heat and stir in cooked noodles and caramelized onions until well combined.

Transfer macaroni mixture to greased casserole dish. In a small bowl whisk together bread crumbs, pecans and 2 tablespoons of butter, melted. Top macaroni mixture with bread crumbs and bake for 5-10 minutes or until golden brown and bubbly.