Fill a large pot with water and bring it to a rolling boil. Add salt and penne pasta, cooking for about 11 minutes, stirring occasionally. Drain the pasta thoroughly and return it to the pot.
Heat olive oil in a large skillet over medium-high heat. Toss in the asparagus, yellow bell pepper, and broccoli, cooking them for 2 to 3 minutes while stirring often. Add the chopped zucchini and continue to cook for 1 to 2 more minutes until vegetables are tender yet retain some crunch. Season with salt and black pepper, then remove veggies from the skillet and set aside.
Place the skillet back on the stove and melt the butter over medium heat. Sauté the minced shallot and garlic for approximately 2 minutes until fragrant. Mix in the lemon zest and vegetable broth, letting the liquid simmer until it reduces by half, about 4 to 5 minutes. Stir in the heavy cream and 2 tablespoons of lemon juice to create a creamy sauce.
Add the frozen peas directly into the pot with the cooked pasta, followed by the sautéed vegetables. Pour the lemon cream sauce over the pasta and vegetables, mixing gently to blend all elements together. Incorporate the Parmesan cheese along with the remaining tablespoon of lemon juice. Finally, fold in the halved grape tomatoes and chopped basil. Adjust seasoning with salt and black pepper to your preference.
Transfer the pasta primavera into a serving bowl or dish. Sprinkle with Italian parsley, extra Parmesan cheese, and a pinch of crushed red pepper flakes for garnish. Serve the dish warm and enjoy.