Cut onions lengthwise into 1/4-inch slices. Place onions and 2 tablespoons olive oil in wide, thick-bottomed sauté pan; cook over medium heat, stirring occasionally, 45 minutes or until onions cook down to about 2 cups. Remove from heat and set aside.
Preheat oven to 350°F. Cook pasta according to package directions until al dente; rinse thoroughly with cold water, drain well, and set aside.
In medium saucepan, over medium heat, melt butter. Once melted, whisk in flour, milk, beef broth, salt and pepper. Continue to whisk mixture and cook over medium heat until sauce thickens to consistency of custard sauce; remove from heat. Whisk in 1 cup of swiss cheese; set aside.
Grease ceramic or glass 9x12x3-inch baking dish; set aside. In food processor,
pulse together bread, remaining olive oil, remaining cheese and thyme leaves until the mixture resembles coarse meal.
In large mixing bowl, mix together pasta, cheese sauce and caramelized onions,
making sure the onion pieces are distributed evenly. Pour mixture into prepared baking dish; sprinkle with bread crumb mixture. Bake 20-15 minutes or until top is golden brown and pasta is heated through.