Pasta: Bring a large pot of salted water to a boil. Add pasta and cook until al dente according to package directions. Drain and set aside,
Preheat oven to 375 degrees. Spray a 9x13 baking dish with non-stick cooking spray. Set aside.
Add 8 tablespoons butter to a large skillet over medium high heat. Stir in onions, salt and pepper. Cook for 15 minutes, stirring often. Reduce heat to medium, add sugar and garlic and continue to cook for 10 more minutes
Add sherry and cook for 3 minutes or until just evaporated.
Stir in flour and cook, stirring constantly for 2 minutes. Slowly add beef broth and thyme leaves and bring to a boil, stirring constantly. Lower heat and let mixture simmer 5 minutes. Remove from heat.
Mix in penne , 2 cups of the shredded swiss cheese and the parmesan cheese. Add to the prepared dish. Top with the remaining one cup shredded swiss. Sprinkle with panko crumbs and one or two tablespoons extra freshly grated parmesan cheese.
Bake for 20-25 minutes until lightly browned and bubbly.