Start with a very large pot of water, about 4 quarts. Bring it to a rapid boil. Add 2 tablespoons of kosher salt and drop in the pasta while the water is at a boil and give it a gentle stir. Stir it occasionally while it cooks. Use the cooking time on the pasta package as a guide to cook until just al dente.
Drain the pasta. Just be sure to save about ¼ cup of the pasta water. If you have a pot with a colander insert, use it to drain the pasta. If not, drain the pasta in a colander set in the sink.
Meanwhile, preheat a large (14-inch) saute pan over medium-high heat, add the oil. When hot, add the onion, garlic, and 1 teaspoon kosher salt and cook, stirring until they begin to caramelize about 10 to 15 minutes. Add the tomatoes, basil, parsley, thyme, 1 teaspoon kosher salt, pepper, and red pepper flakes. Reduce the heat to medium-low and cook for 5 to 7 minutes, occasionally tossing, until the tomatoes begin to soften but don't break up.
As soon as the pasta is cooked, lift the pasta out of the water with tongs, allowing most but not all of the water to drain back into the pot, and add all the pasta to the sauce.
Cook for one minute, adding pasta water to the sauce with a ladle just enough to keep the pasta moist. Taste and adjust the salt if needed. Transfer the Veggie Spaghetti with Tomatoes and Basil to a serving platter or individual plates and top with grated parmesan cheese. Garnish with more chopped basil. Serve hot. Enjoy!