Bring a large pot of salted water to a boil and add penne pasta. Cook for about 11 minutes or until tender.
While pasta is cooking, heat oil in a large skillet on medium-high heat. Add onion and cook for about 2-3 minutes. Add asparagus, mushrooms, and squash and cook for 5 minutes. Finally add tomatoes, garlic, basil, black pepper, salt, and red pepper flakes and cook for about 1 minute.
Drain pasta and stir into vegetable mixture with ½ cup parmesan cheese. Serve onto plates and top pasta with remaining cheese and lemon wedges.