01 - Preheat oven to 400°F. Grease a 2-quart baking dish with butter or cooking spray.
02 - In a large skillet, heat 3 tbsp butter and 1 tbsp olive oil 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 until mostly evaporated, about 3 minutes. Remove from heat and set caramelized onions aside.
04 - Bring a large pot of salted water to a boil. Cook pasta until just al dente according to package directions. Drain well and set aside.
05 - In the same skillet (wipe clean if necessary), melt 2 tbsp butter over medium heat. Whisk in flour and cook for 1-2 minutes until lightly golden. Gradually whisk in milk and cream, stirring constantly until mixture thickens, 3-5 minutes.
06 - Reduce heat to low. Stir in Gruyère, cheddar, and Parmesan cheeses until completely melted and smooth. Season with black pepper.
07 - Fold caramelized onions and drained pasta into the cheese sauce, mixing well to coat everything evenly.
08 - Pour the pasta mixture into the prepared baking dish, spreading it into an even layer.
09 - In a small bowl, combine panko breadcrumbs, melted butter, and grated Gruyère cheese. Mix until evenly combined.
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. Let rest for 5 minutes before garnishing with fresh parsley and serving.