Oh, I think I clarified this in another question (I can’t remember but it must have been answered in a different topic in the Crystal Fragments section… anyways)
Technically it was the fal’Cie who created the Arks, but it was under Bhunivelze’s order to do so. He wanted the Arks to create and prepare armies against Mwynn and the unknown threat in the Invisible World. You can easily deduce it from this Analect:
X: The Menace Beyond
They say the fal’Cie made the Arks in preparation for battle against the menace that lurks beyond. Where is this “beyond” of which they speak? Do they mean Cocoon, and the demons that dwells within? If so, they are mistaken. The legends of the Arks date far before that sphere was even crafted; whispers even hint at Arks displaced around the time of Cocoon’s creation, spirited away to be hidden in its shell.
What, then, is the “menace”? What distant threat confronts us, and to what purpose? The gods vanished from this place. Are they now residents of the “beyond”?
—On the Nature of Fal’Cie
…and from our knowledge of the core mythology.
I have confused people because I kept saying that “Bhunivelze made the arks.” I should have clarified that I didn’t mean technically.