Preheat oven to 425 degrees F.
In a small saucepan, over medium-low heat, melt the butter and cook until it is just beginning to brown. Immediately add the thyme and garlic. Cook for 2 minutes, stirring to prevent the garlic from browning. Add the cream, raise the heat to medium, bring to a slow simmer and reduce the cream by 1/3, about 2 minutes. Add the cheese and stir until the cheese melts and the mixture is smooth, season, to taste, with pepper. Pour the sauce into a fondue pot and set over a candle to keep hot.
Place the platter of veggies and skewers alongside and serve immediately.
Using a small paring knife peel and halve the cipollini. Heat the olive oil in a large saute pan over high heat until hot but not smoking. Add the onions and season with salt and pepper. Caramelize the onions over high heat for about 5 minutes, transfer pan to the oven and continue to cook for about 8 to 10 minutes until the onions are nicely caramelized and fully cooked throughout, remove from pan to a plate and let cool slightly. Arrange the cherry tomatoes and onions on a platter with skewers for dipping.