Preheat oven to 350F.
With a sharp paring knife, core the Brussels sprouts and separate the leaves. Place in a large bowl.
Bring a large pot of water to a boil. Salt water and par-boil the leaves 2 minutes or so to tender crisp. Remove with a spider, drain and cool, and dry on a kitchen towel. Add more water to fill the pot back up for the pasta and return to boil.
Heat a saucepot over medium heat with the EVOO and brown bacon; remove and drain. Pour off most of the drippings then add butter and melt. Add onions and garlic, stir 5 minutes, add a little salt and pepper, stir in flour and cook 1 minute. Whisk in wine to deglaze; whisk in stock and then milk. Cook to thicken and season with nutmeg to taste. Reduce heat to low.
Boil pasta 5-6 minutes to just shy of al dente; drain.
Stir 2/3 of the cheeses into sauce in a figure-8 motion. Drain pasta, toss with Brussels sprouts, bacon and sauce, and pour into a baking dish. Top with remaining cheese and heat through in the oven, about 10-12 minutes.