A Theory On Why Jon's Empathy Made Him The True Pupil
The Eye sees all, knows all, and forever craves more knowledge. But knowledge is hollow without understanding. There's a difference between reading "fire is hot" and burning your finger touching a candle. Fear is only a concept, until it is *felt*.
Unlike the Eye's sister fear, the Web, the Eye sees what was and is in pure cold objectivity, and never understands enough to use this knowledge to form new information, such as predicting the future.
The Eye needs understanding. To gain this understanding, it needs a conduit.
Jonah Magnus, Elias, is not this conduit. Jonah is a coward and never engages directly, choosing to manipulate and watch the suffering of others from a distance. He is detached from all of it in his selfish greed. He is not committed to the Eye save for how it serves his own desires. This is easily discerned from the fact that he himself could have undergone the "trials" Jon went through to become the catalyst of the change but instead forced Jon to do so.
Then, there is Jon. In a sense cowardly, yes, but unlike Jonah, he has - albeit often unwillingly - *faced* his fears, and through statements *felt* the suffering of others. He is a being of empathy, of understanding. And as Jon becomes more and more embedded in his existence as The Archivist, his empathy grows. His portrayal gradually changes from a snide, detached academic, to a man struggling to hold on to what's left of his humanity and the people he cares about. The same season that he begins to prioritize helping his friends (pulling Daisy from the coffin, removing the bullet from Melanie), he completes his transformation into this conduit - finalized by opening up and rescuing the person he loves, Martin.
Another Tumblr post emphasized that Jon during the apocalypse is not the antichrist, but in fact an allegory of Christ Himself. It occurred to me reading that post that also, much like Christ, Jon is both man and god, and feels all of the fear and pain of the trapped souls in the world. A bridge between divine fear and human suffering.
When Jon uses his power to "smite", his weapon is empathy. He forces the avatar to feel and know the fear they have inflicted - unlike him, they are unable to bear this suffering, and disappear.
The Eye knows, and Jon feels. And that is why he is the true Pupil, because unlike Jonah, he can make the Eye's knowledge of human fear whole.