Melt butter in a large, deep skillet or Dutch oven over medium heat. Add sliced onions and sugar, and cook for 20-25 minutes, stirring occasionally, until onions are deep golden brown and caramelized.
Add beef broth, water, thyme, salt, and pepper to the pot. Increase heat to high and bring to a boil.
Stir in the orecchiette pasta, reduce heat to medium-high, and cook uncovered for 12-15 minutes, stirring frequently, until pasta is tender and most of the liquid has been absorbed.
Remove from heat and stir in 1 cup of the Gruyère cheese until melted. Serve immediately topped with remaining cheese.