He is stated to have kept surrounded only by hurt and abused Pokemon. His room is full of toys that have been damaged by things like claws, suggesting the Pokemon he was with had a bit of a violent temper. The fact that he lived his entire life isolated from the real world is itself a form of abuse.
When Plasma's plan is done with, Ghetsis furiously insults N, calling him a freak, taunting him over his inability to understand humans (a result of his isolation), and proceeds to battle you using a team that seems tailored to defeat N's. The fact that he has Kyurem attack you in BW2 shows his regard for human life, and has certain implications for what would happen when N's usefulness is gone.
I generally agree, in fact wording it the way you did emphasises the Nightmare Fuel-ness of it, but I didn't get the impression that the Pokemon were violent- just that N had no human friends so he would play with his Pokemon like children play with each other, so the toys were damaged just because they were played with.
Screw the games. My dream about Pokemon last night is the most dark.
An antagonist kidnapping Gym Leaders by trapping them in badges, doing the same to Ash's Pikachu, then killing it before he catches up with the villain. Then Ash trying to kill the antagonist with his bare hands, and nearly succeeding, then I woke up.
I think you have a Darkrai infestation.
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