In a large pot, boil enough water and cook the penne according to the package directions. Drain the cooked pasta and keep it aside. I would reserve about a cup of pasta water to use later.
Preheat the oven to 375 F.
In a large pan, heat the olive oil and sauté the onions until translucent. Now add the garlic and cook for 30 seconds more. Add the bell pepper, broccoli, and crushed red peppers and cook until the vegetables are softened.
Now add the marinara sauce and let it heat up. Also, add about ½ cup of reserved pasta water and let it come to a simmer. Break the cream cheese into small pieces and add them to the simmering sauce. Let it dissolve and then simmer the sauce for about 5-10 minutes, stirring occasionally.
Add the cooked pasta to the sauce mixture and stir well to coat. At this point, if the sauce appears too thick, add a little bit more of the reserved pasta water.
Transfer the pasta to a greased 9 x 13 pan and spread it evenly. Top with the grated mozzarella and parmesan cheese.
Bake for about 20-25 minutes until the pasta is bubbly and the cheese has melted.
Serve the baked vegetable pasta hot!