Fill a large pot with water and bring it to a rolling boil. Season the water with salt, add the penne, and cook for about 11 minutes while stirring occasionally. 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. Add the asparagus, yellow bell pepper, and broccoli, sautéing for 2 to 3 minutes, stirring now and then. Toss in the zucchini and continue cooking for 1 to 2 minutes until the vegetables are tender but retain some crunch. Season with salt and black pepper, then transfer the vegetables to a bowl.
Return the skillet to the stove and melt the butter over medium heat. Add the minced shallot and garlic, cooking gently for roughly 2 minutes until fragrant. Mix in the lemon zest and vegetable broth, letting the mixture simmer until it reduces by about half, which takes around 4 to 5 minutes. Stir in the heavy cream and 2 tablespoons of lemon juice.
Fold the frozen peas into the pot with the drained pasta. Add the sautéed vegetables, then pour the lemon cream sauce over everything. Stir everything together until fully coated. Mix in the Parmesan cheese and the remaining tablespoon of lemon juice. Carefully fold in the grape tomatoes and chopped basil. Adjust seasoning with salt and black pepper as preferred.
Transfer the completed pasta primavera to a large serving bowl or platter. Garnish with the chopped Italian parsley, extra Parmesan cheese, and a sprinkle of crushed red pepper flakes. Serve the dish warm and enjoy.