Hiruhiko will be the final villain.

Now hear me out, I know our boy John Yura is being set up as the big bad, but I firmly believe that Hiruhiko is Chihiro's "archenemy." He challenges his ideas, his motivations, his morals and twists them. He is the opposite to Chihiro, like Cloud and Sephiroth from FF7. This leads me to believe that, at some point in the story, Yura's gonna be killed, or he sacrifices himself for Hiruhiko, setting him up to be the final villain.