Preheat oven to 425 degrees F.  Line 2 large baking sheets with aluminum foil, and coat with cooking spray.  Toss broccoli, cauliflower, cubed squash, and Brussels sprouts with olive oil, and season with salt.  Spread vegetables in an even layer on prepared baking sheets.  Cover with foil. Bake at 425 degrees 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 heat.  Add chopped onion, and cook 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 stir until cheeses are melted.  Add cooked pasta, and mix well; fold in roasted vegetables.