01 - Preheat oven to 400°F. Grease a 2-quart baking dish with butter or cooking spray.
02 - In a large skillet, heat 3 tablespoons butter and 1 tablespoon olive oil over medium heat. Add sliced onions, thyme, and 1/2 teaspoon salt. Cook, stirring frequently, for 20 to 25 minutes until deeply caramelized and golden brown. Lower heat as needed to prevent burning.
03 - Stir in minced garlic and cook for 1 minute until fragrant. Add white wine and Worcestershire sauce, scraping up browned bits from the bottom of the skillet. Simmer for 3 minutes until mostly evaporated. Remove caramelized onions from heat and set aside.
04 - Bring a large pot of salted water to a boil. Cook pasta according to package directions until just al dente. Drain well and set aside.
05 - Wipe the skillet clean if needed. Melt 2 tablespoons butter over medium heat. Whisk in flour and cook for 1 to 2 minutes, stirring constantly. Gradually whisk in milk and cream, stirring constantly until the sauce thickens, 3 to 5 minutes.
06 - Reduce heat to low. Stir in Gruyère, cheddar, and Parmesan cheeses until melted and smooth. Season with black pepper.
07 - Fold caramelized onions and drained pasta into the cheese sauce, mixing thoroughly to combine all ingredients.
08 - Transfer the pasta mixture to the prepared baking dish, spreading evenly.
09 - In a small bowl, combine panko breadcrumbs, melted butter, and Gruyère cheese. Mix until breadcrumbs are evenly coated.
10 - Sprinkle the breadcrumb mixture evenly over the pasta. Bake for 20 minutes until the topping is golden brown and the sauce is bubbling around the edges. Let rest for 5 minutes before garnishing with parsley and serving.