Preheat oven to 375 degrees and grease a 3 quart baking dish.
Cook pasta 2 minutes less than package directions.
While pasta cooks, in a medium saucepan over medium heat, melt butter. Ass flour and shallot, and cook 2 minutes, stirring frequently. In a slow stream, add milk,whisking constantly. Increase heat to medium-high and bring to simmer. Cook for 2-4 minutes until thickened.
Off heat, add salt and cheeses, stirring until cheese is just melted. Combine pasta with cheese sauce, broccoli and cauliflower, and pour the mixture into a baking dish.
Bake until sizzling and lightly browned on top, about 20 minutes. Let stand at least 5 minutes before serving.