Bring a large pot of salted water to a boil over high heat. Add the pasta and cook until tender but still firm to the bite, stirring occasionally, about 8 to 10 minutes. Drain pasta reserving 1 cup of the pasta cooking liquid.
In a large bowl combine the 2 cups Aiago cheese, creme fraiche, Parmesan, thyme, salt, pepper, cooked pasta, and pasta cooking liquid. Gently toss until all the ingredients are combined and the pasta is coated. Place the pasta in a buttered baking dish and sprinkle with the remaining 1/4 cup asiago cheese. Bake until golden on top, about 25 minutes. Let sit for at least 5 minutes and serve.