When you think about it, Jon and Martin’s experiences with the Institute were roughly the same. The only difference is in their behaviour, and in how each of them handled themselves.
Oh Martin had to work alongside Peter Lukas and fulfill all his wishes and orders, even if they didn’t sit right with him? Jon had to do the exact same for Elias.
Martin worked his ass off to protect his coworkers from a big unknown evil, and isolated himself from everyone in the process? Jon went through the same with his Gertrude murder investogation.
Martin had no one left in the world to care for him, especially after his mother died? Jon was alone too - at a certain point everyone in the Archives resented him, he was an orphan without any living family members, and the only person he could turn to was an ex girlfriend who really didn’t like him all that much.
Jon and Martin even have similar self-esteem issues. They are both depressed.
But somehow Martin always ends up as the fandom’s poor mistreated boy, and all Jon ever gets to be is a wet blanket antichrist boyfriend whose only redeeming characteristic is his undying love and devotion for the former man.