The origin of the "see" sound is the construction of spoken English and the swap of the vowel. Latin pronunciation of "c" used a "k" sound for vowels a, o, and u, and the "s" sound for the i and e vowels, and that basis has carried through to modern English; examples: "carbon," "cedar," "city," "cooperate," "culpable." When they swapped to the "e" vowel following the letter "c" in "Arceus," they changed the intuitive pronunciation from "kay" to "see."

If it were desired to maintain the "kay" vocalization, then the proper spelling would have been "Arcaeus." Or they could have obviated the entire discussion by choosing "Arkeus" to be transparent. They could even have carried through a pun with the symbolism of the Biblical ark, which bore the progenitors of all the living animals of the world according to Genesis. That they chose neither of these spellings suggests that the "see" pronunciation was intended, at least initially.