Preheat oven to 400F and grease a 9x13 (or large round) baking dish.
In a large skillet, heat the oil over medium/high heat. Add the onion and garlic and cook until fragrant and translucent, about 3-4 minutes.
Add the squash and zucchini, seasoning with salt and pepper to taste. Saute until the veggies are soft and beginning to brown, about 6 minutes.
Add in the tomatoes and cook for just 2-3 minutes, until heated through but still retaining their shape.
Transfer all the veggies to a large bowl and stir in the cooked pasta. Set aside.
In a small saucepan, heat the butter over medium heat. Once melted, stir in the flour and cook, stirring, for 2 minutes. Slowly add in the milk and bring to a boil, then reduce immediately to a simmer. Stir often for 5 minutes or until thickened.
Add in the grated parmesan and the cream cheese and stir until fully combined. Season with salt and pepper to taste.
Pour the cream sauce into the bowl with the pasta, and stir to coat all the pasta and veggies.
Pour the pasta into the baking dish and sprinkle with the shredded mozzarella. Cover with the bread crumbs.
Bake for 15 minutes or until the entire dish is heated through and the bread crumbs are browned.