So on the line that N believes himself to be perfection, I made a comment on another thread on how Ghetsis views himself as perfection
It is possible Ghetsis passed on his sentiments of perfection to N as well. Combine N's distance from humans, closeness with Pokemon, the suffering he witnessed, and the belief he is perfection. Ghetsis just created a person impervious to seeing the truth."What?! I created Team Plasma with my own hands. I'm absolutely perfect! I AM PERFECTION! I am the perfect ruler of a perfect new world!"
This is why I think N's dragon is the dragon of truth, Reshiram shows itself to N because N wishes to discover the truth deep down, but his vision has been occluded. Zekrom sides with the protagonist because the truth is not an absolute in either direction (that ALL Pokemon are better with people) but would fight for the ideal that humans and Pokemon could get along--something that can only be accomplished if they are not separated.