In a large bowl, combine ground beef, panko, egg, garlic, salt, pepper, and half of the thyme leaves; mix until just combined and form into 1-inch meatballs.
In a large oven-safe skillet over medium heat, melt butter and olive oil. Add the sliced onions and cook, stirring occasionally, for 40 minutes until deeply caramelized and brown.
Remove onions from the skillet and set aside. Increase heat to medium-high and add meatballs to the skillet, searing until browned on all sides, about 5-7 minutes. Remove meatballs from the pan.
Add the caramelized onions back to the skillet and sprinkle with flour. Stir for 1-2 minutes to cook out the raw flour taste.
Gradually whisk in the beef broth, Worcestershire sauce, and balsamic vinegar. Bring to a simmer.
Return the meatballs to the skillet, cover, and simmer for 10 minutes until the meatballs are cooked through and the sauce has thickened.
Preheat the oven broiler. Remove the lid from the skillet, sprinkle shredded Gruyère cheese over the meatballs, and broil for 2-3 minutes until the cheese is melted and bubbly.
Garnish with remaining thyme and fresh parsley before serving.