Cook macaroni in unsalted water according to package directions until tender, but still firm. Drain well.
In a medium saucepan, cook the onion in the 4 teaspoons butter until tender but not brown. Stir in the flour and the pepper. Add the milk all at once. Cook and stir until the mixture is slightly thickened and bubbly. Remove from heat. Add the Emmentaler cheese, stirring until melted (the mixture may appear slightly curdled). Stir in the cooked macaroni. Transfer the mixture to a 1 1/2-quart casserole.
In a small saucepan, melt the 2 tablespoons butter. Stir in the bread crumbs and Parmesan cheese. Sprinkle atop macaroni mixture.
Bake in a 350°F oven about 20 minutes or until heated through. Let stand for 5 minutes before serving. If you like, garnish the casserole with fresh thyme.