N, his sisters and his presumably deceased mother are all Zoroarks owned/fostered by Ghetsis.

What triggered N wanting to liberate Pokemon from humans was seeing his mother (a pokemon) abused (potentially killed) by his "father" Ghetsis. We know Ghetsis abuses N too, so that's why he obeys out of fear. But his end goal is to free all Pokemon and eventually defect from his father and Plasma when that goal is reached. This explains why N can understand Pokemon and why he doesn't feel guilty being a trainer.
>Zoroark can talk while disguised, seen in BW2
>Memory Links are told in the perspective of the person you talk to. One Memory Link has you talk to a Zoroark, and then the flashback is shown in N's perspective. The logical conclusion is that that Zoroark is N.
>N leaves his dragon because he believes that the Dragon's duty is to help "humans that seek ideals/truth." After that, he talks about how he's seeking an ideal/truth. Since he's still seeking his ideal/truth, wouldn't that mean that he's leaving the Dragon because he's not a human?
>N's room has "scratch marks from a Pokemon" when you examine his halfpipe. Makes most sense that they're from N himself since he doesn't really carry around Pokemon most of the time.
>A few lines where him, Ghetsis, and others refer to his life "learned to live as a human" or how "doesn't have a human heart," etc.