In a medium mixing bowl, combine the ricotta, chopped basil, lemon zest and red pepper flakes until well combined. Set aside.
Heat the oil in large skillet over medium heat. Add the onions and cook, stirring frequently for 3-4 minutes or until they start to become translucent. Add the zucchini and the yellow squash and cook, stirring frequently for about 5-6 minutes.
Stir in the tomatoes and season with Italian seasoning and salt and pepper to taste. Cook, stirring often for about 5 additional minutes or until the zucchini and yellow squash become tender.
Stir in the garlic and cook for about a minute or until the garlic become fragrant. Remove from the heat.
Meanwhile, while the vegetables are cooking, cook the pasta in salted water according to package directions until al dente. Drain the pasta reserving 1 cup of cooking water.
Return the cooked pasta to the pot and turn the heat to medium low. Stir in the ricotta mixture and 1/2 cup of the cooking water. Toss well to coat the pasta evenly. Next, stir in the cooked vegetables and the Parmesan cheese and toss gently to combine.
Season to taste with salt and pepper. The pasta should look creamy. You can add additional pasta water if necessary.
Scoop pasta into serving bowls and serve immediately drizzled with basil pesto and additional Parmesan cheese (optional).