It would be Team Plasma, because they were actually nasty, convincing people that their intentions were for the better of pokemon and humans,but wanting rule Unova in the absence of pokemon with the everyday folks. If I'd be a member, I'd be thinking that I'm fighting for a good cause. Also, the leadership's ultra twisted plan was a well kept secret even within the organisation, in fact it was hidden from the leader's son, N himself.
Speaking of N, he's an awesome anti-protagonist. His childhood was tragic. He doesn't want to be evil, but due to his innocence, ends up performing such actions. His vision was to change the world without force as using force would cause resistance to the change. He was ready to stand for his pokemon friends.
"I will show you that my love for my friends permeates every cell of my body." -N