Apparently, N was an orphan abandoned in the woods and raised by Pokémon, which then was found by Ghetsis, who took him and used him for his plans. Anyway, if we consider also the appearance similarity between them, I wouldn't be surprised if in reality he is really his father and abandoned him in the woods appositely as an experiment to recreate the hero of the legends. If I remember well, Ghetsis said that he permitted only Pokémon hurt by humans to make contact with N, to warp his perception of the world and the relations between humans and Pokémon, making him believe that Pokémon and humans shouldn't stay together.
Honestly, the villains in Pokémon are not very well written. There is Giovanni, but it's more because he is iconic. In fact, his story is pretty generic (which is not necessarily a bad thing). Otherwise, I would say N, but in this case, after knowing his story, is difficult to consider him a villain. So I'll settle with Ghetsis, since he is the reason for which we have N, and because the story of Black and White is the best of all the Pokémon games also thanks to him.