Preheat oven to 450 degrees. In a large roasting pan, toss together onions, oil, sugar, thyme, 2 teaspoons salt, and 1/4 teaspoon pepper. Cover tightly with foil; cook until steamed, about 30 minutes. Uncover; cook, stirring every 30 minutes, until onions are golden brown and caramelized, 1 to 1 1/4 hours more.
Transfer onion mixture to a large saucepan (reserve roasting pan); stir in broth and 6 cups water. Bring to a boil; reduce heat to a simmer. Cook until liquid has darkened, about 20 minutes.
Meanwhile, deglaze the roasting pan with wine: Place the pan over medium heat; add wine. Scrape bottom of pan with a wooden spoon or scraper to loosen any browned bits. Simmer until reduced and syrupy, about 2 minutes. Pour liquid (and browned bits) into soup. Season with salt and pepper. (If freezing, let cool completely before transferring to airtight containers, leaving 1 inch at top.)
If desired, make the cheese toast: Heat broiler. Place bread on a baking sheet; top with Swiss cheese. Broil until cheese is bubbly and golden brown, 2 to 3 minutes. Cut each slice into four triangles.
To serve, divide soup among bowls; garnish each with two triangles of cheese toast, if desired.
To cut onion slices, halve through the root end; peel back skin. Place halves, cut sides down, on cutting board. Trim both ends; thinly slice onion lengthwise. To slice onions quickly, use a food processor fitted with a slicing blade (instead of a knife).