Jon and Jonah being soulmates wouldn’t fix anything. it would, in fact, makes everything worse and more tragic which is why I love it
Jonah would know that Jon is his soulmate and intentionally keep away. he wouldn’t let the Mother of Puppets control him (I imagine she would be the one responsible for soul marks since it deals with fate/predetermination/loss of control. I have a lot of thoughts of how soulmates and Fears mix, please ask me about it). Jonah would view the soul mark both as an approval of his plan and also a mockery of his desire to not have a soulmate
I see young Jonah first wishing for a soulmate due to the societal influence before slowly starting to despise the very concept of it, of being controlled like that, especially after learning about the Web. Jonah would be so smug about not having a soul mark until Elias Bouchard wakes up to ‘Jonathan Sims’ written neatly on his wrist
Jon wouldn’t be interested in finding his soulmate at first. the name on his wrist says Jonah Magnus, so what if the only Jonah Magnus he can find died in the 19th century. it must mean his soulmate has yet to change their name legally, making it harder to find them. it had no influence on him joining the Magnus Institute, he would swear when asked
later he would genuinely hate having a soulmate. both because of the Web and because it hurt “for some reason” to know that Jonah has known the entire time, that he made no mention of it, that he didn’t want Jon. and Jon definitely isn’t bitter about it, he definitely doesn’t want Jonah nor does he wants Jonah to want him
(and Jonah wants him, wants Jon more than he predicted but wanting isn’t the same as choosing and Jonah Magnus is well practiced in the art of choosing himself over anyone else)
