Preheat oven to 400º. Line 2 baking sheets with parchment paper.
Toss cauliflower in 2 tablespoons olive oil and salt and pepper. Place on one of baking sheets. Do the same with broccoli. Bake for 10 minutes, reposition and bake an additional 10 minutes. Remove when tinged with brown.
Cook pasta in large pot of salted water. Drain.
Heat a very large pan over medium heat. Add 1 tablespoon olive oil and pancetta and cook, stirring occasionally for about 4 minutes, until brown and crispy. Add onions and thyme and cook unit onions are tender. and slightly brown. Sprinkle the flour over the top and stir for 1 minute.
Gradually stir in flour and increase heat to medium-high bringing it to a simmer. Reduce heat to medium and gradually stir in milk and cream, heat to simmer, stirring often for about 4 minutes or until it is lightly thickened. Remove from heat and add cheese, stirring until melted. Season with salt and pepper.
Add pasta and vegetables and pour into prepared pan. Melt butter in small bowl and add panko crumbs to it and sprinkle over the top of the pasta. Bake for 10 minutes or unit the crumbs are golden. Let sit for 5 minutes before serving.