Fill a large pot with salted water and bring it to a rolling boil. Add the penne pasta and cook, stirring every so often, until it is tender, about 11 minutes. Drain the pasta thoroughly and return it to the pot.
While the pasta cooks, warm olive oil in a large skillet over medium-high heat. Toss in the asparagus, yellow bell pepper, and broccoli, sautéing for 2 to 3 minutes with occasional stirring. Add zucchini and continue cooking for another 1 to 2 minutes until the vegetables are tender but still crisp. Season with salt and black pepper then transfer the cooked vegetables to a bowl.
Return the skillet to the stove and melt the butter over medium heat. Sauté the minced shallot and garlic until fragrant and soft, about 2 minutes. Add lemon zest and vegetable broth; let the mixture simmer until the broth volume halves, which will take approximately 4 to 5 minutes. Stir in the heavy cream along with 2 tablespoons of lemon juice.
Mix the frozen peas into the pot with the pasta followed by the sautéed vegetables. Pour the creamy lemon sauce over the pasta and veggies and combine everything gently. Add the shredded Parmesan cheese and the last tablespoon of lemon juice. Fold in the halved grape tomatoes and chopped basil. Adjust seasoning with salt and black pepper to your taste.
Transfer the pasta primavera to a serving dish and top it with the Italian parsley, extra Parmesan, and a sprinkle of crushed red pepper flakes. Serve immediately while warm.