Preheat oven to 425°F. Line 2 large baking sheets with aluminum foil, and coat with olive oil spray. Toss broccoli, cauliflower, squash, and Brussels sprouts with olive oil, and season with salt. Spread vegetables in an even layer on prepared baking sheets. Bake at 425°F for 25 to 30 minutes, stirring vegetables and rotating pans halfway through cooking time, until vegetables are soft and have begun to brown around the edges.
While vegetables roast, bring a large pot of water to a boil. Cook pasta according to package directions, omitting fat and salt. Drain, and set aside.
Melt butter in a medium saucepan over medium. Add onion, and cook over low about 2 minutes. Add flour, and cook another minute or until the flour mixture is golden and well combined. Add milk and broth; whisk, increasing heat to medium-high until mixture comes to a boil. Cook about 3 to 4 minutes or until it thickens slightly, and then season with pepper.
Remove pan from heat; add cheeses, and mix well until cheeses are melted. Add cooked pasta, and mix well; fold in roasted vegetables.
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