Preheat the oven to 375F degrees. Bring a medium pot of salted water to a boil. Add the noodles and cook until just al dente (about 6 minutes), according to package directions. Drain and set aside.
Meanwhile, heat the butter in a saucepan over medium heat. Add the flour and cook to make a golden brown paste, stirring often. Gently whisk in the milk and cook, stirring until the milk thickens, about 5 minutes. Stir in the fontina, Swiss cheese, and 2 tablespoons of Parmesan, until melted. Add the 1/4 teaspoon cayenne pepper, about 1/2 to 1 teaspoon of salt, and freshly ground pepper to taste.
In a large bowl, toss together the cooked noodles, cheese sauce, peas and asparagus. Stir until the noodles and vegetables are coated. Stir in the basil and 1/2 cup of the mozzarella balls. Place in a 9x9-inch baking dish. Then sprinkle the remaining 1/4 cup mozzarella balls over the top.
Mix together the breadcrumbs, Parmesan cheese, and another 1/4 teaspoon cayenne pepper. Bake for 20 minutes or until hot and bubbly. Remove from oven and let set for 5 minutes for the sauce to thicken back up before serving.
Optional after the 20 minutes of baking- Even though the mac and cheese is ready to go after 20 minutes in the oven, here's a tip for increasing the flavor and gooey richness even more. If you have time, after the 20 minutes in the 375F degree oven, turn the temperature down to 200F degrees, cover the baking dish tightly with foil and let the dish stay in the oven for at least an extra 30 minutes, and if you have A LOT of time, turn the oven to 185F degrees, cover the dish and let it sit in the oven for another hour. This makes all the flavors just continue to seep into the noodles and become even more delicious.
Make ahead- You can also make the mac and cheese and don't top it with the panko Parmesan mixture yet, but cover the dish with foil and refrigerate overnight. Then add the topping just before baking and bake for 25 minutes in 375F degree oven.