Or, perhaps, because ntr is taboo, we subconsciously think that the person who is cheating must be depraved, evil or generally a jerk in several ways and Arato is definitely the biggest jerk here so maybe he fills that stereotype we are all harboring better than Kendo, thus his route having bigger ntr vibe.
I want to make an argument about how fucked up is Kendo and how his NTR is 100% more cruel than Aratos.
Kendo doesnt use cheaps tricks like drugs but is keen on exploting peoples weakness to get what he wants.
Take Hanako for example, she was a woman sheltered and sofocated by an overprotecting parent that wanted the freedom to explore more, try new things and become a better version of herself. Kendo used that to equate those desires of Hanako with becoming his fuck toy and giving away her virginity to a man she barely knew.
And the same occurs with Satoshi and Mary. He is in a position of trust as a "host/benefactor" of their vacation and being Satoshis family, that allows him to be privy to Satoshis failures as a boyfriend and be the shoulder for Mary to lean on. Kendos experience would've made it easy for him help both of them to understand each other but instead uses those situations to chip away at Marys defenses until she wants him as much as he does. Not satisfied with getting to fuck her he wanted to steal her, to the point he inmidiately fucked Mary outside Satoshis room after they had make up sex so she couldnt even start to think about backpedaling on their affair.
Even in the Arato situation he scolds them for getting themselves into that like a good caring adult should and then the same night inmidiately uses it to break the last traces of resistance in Marys mind. Kendo has nothing but disgust for Aratos methods while at the same time having no qualms on taking advantage of the situation that Arato setted up.
Post Arato Kendo feelings becomes outright cruel towards Satoshi with justifications that are rather hypocritical because while he correctly points out Satoshi faults and flaws, he fails to admit how his affair with Mary exacerbated Satoshis worst traits and , like any man wanting some pussy, exonerates Mary of any blame.
And lets remember that he does all this not to a random young man that he never met before but to his so called "favorite nephew" and betrayed the trust of him and Mary to exploit the failling on their 3 months old relationship.
I have no doubt that if Satoshi is forced to confront the full extent of what Kendo did, that it will be 100 times more crushing that whatever Arato ends up doing, wich is why i have higher hopes for his route because i feel its gonna be 10/10 NTR material while Arato is a solid 8.
Arato is more sterotypically evil but Kendos is more insidious, he is no stereotype because he is on a league of his own. Personally i would rather deal with a person who openly acts as a douchbag than someone that smiles at you while giving you a handshake with one hand and stabs you in the gut with the other, because if this is what "King" Kendo is willing to do to his own nephew then everyone else in the world might be fair play.