How to Make It
Heat oven to 425° F. Toss the broccoli, cauliflower, tomatoes,1 tablespoon of the oil, and 1/4 teaspoon each salt and pepper on a rimmed baking sheet. Roast, tossing once, until tender, 14 to 16 minutes. Remove from oven.
Meanwhile, cook the pasta according to the package directions; drain.
Heat the remaining 2 tablespoons of oil in a medium pot over medium heat. Add the flour and cook, whisking, for 30 seconds, Slowly whisk in the milk. Cook, stirring occasionally, until thickened, 5 to 7 minutes. Remove from heat and stir in the Cheddar, vegetables, and pasta.
Transfer the mixture to a 2-quart baking dish. Top with the pepper jack and broil until golden brown, 2 to 3 minutes.