Preheat oven to 400°F 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.
2 tablespoons light olive oil, ½ cup diced yellow onion, ¼ red onion, 3 cloves garlic
Add the squash and zucchini, seasoning with salt and pepper to taste. Sauté until the veggies are soft and beginning to brown, about 6 minutes.
1 cup chopped zucchini, 1 cup chopped yellow squash, Kosher salt and freshly ground black pepper
Add in the tomatoes and cook for just 2-3 minutes, until heated through but still retaining their shape.
1 cup cherry tomatoes
Transfer all the veggies to a large bowl and stir in the cooked pasta. Set aside.
¾ pound cooked penne pasta
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.
1 tablespoon salted butter, 1 tablespoon all-purpose flour, 1 cup skim milk
Add in the grated parmesan and the cream cheese and stir until fully combined. Season with salt and pepper to taste.
¾ cup grated Parmesan cheese, 4 tablespoons low-fat cream cheese
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.
1 cup shredded mozzarella cheese, 1 cup Panko bread crumbs
Bake for 15 minutes or until the entire dish is heated through and the bread crumbs are browned. Garnish with thyme sprigs.
Fresh thyme sprigs