01 - Preheat oven to 400°F. Grease a 2-quart baking dish with butter or cooking spray.
02 - Heat 3 tbsp butter and 1 tbsp olive oil in a large skillet over medium heat. Add sliced onions, thyme, and 1/2 tsp salt. Cook, stirring frequently, for 20–25 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 from heat and set caramelized onions 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 tbsp butter over medium heat. Whisk in flour and cook for 1–2 minutes to form a roux. Gradually whisk in milk and heavy cream, stirring constantly until the sauce thickens, 3–5 minutes.
06 - Reduce heat to low. Stir in Gruyère, sharp cheddar, and Parmesan cheeses until completely melted and smooth. Season with 1/4 tsp black pepper.
07 - Add caramelized onions and drained pasta to the cheese sauce. Fold together gently until well combined and evenly coated.
08 - Pour the mixture into the prepared baking dish, spreading it evenly.
09 - In a small bowl, combine panko breadcrumbs, melted butter, and grated Gruyère cheese. Mix until the breadcrumbs are evenly coated.
10 - Sprinkle the breadcrumb mixture evenly over the pasta. Bake for 20 minutes until the top is golden brown and the sauce is bubbling around the edges.
11 - Let the dish rest for 5 minutes before serving to allow the sauce to set slightly. Garnish with chopped fresh parsley if desired.