As over dramatic as my theory is, I feel like it's an interesting one nonetheless.
I personally think that Ghetis is N's uncle, and he killed N's father in a Hamlet-esque political squabble.
It's generally believed that the Harmonias are related to the twin brothers that awakened the dragons. What if Ghetis and N's father are a reincarnation of this squabble? Perhaps one of them represented truth, and the other represented ideals, and they themselves fought each other for power over the Harmonia name. N's father was perhaps the one destined to take the throne, for whatever reason, or maybe it's because he had a son which Ghetis had no offspring to pass on the crown to. It wouldn't exactly be out of Ghetis's character to murder in order to gain power. It also wouldn't be too unbelievable that he would leave his nephew out in the wilderness to die, and not give a second thought.
Ghetis adopted the two girls as a way to secure his rights to his throne, but found out that without Harmonia blood, they didn't count. This is where his scheme to create Team Plasma came in. Bear in mind that the "royal blood" no longer has any power, and is only really known to the Harmonia's, and perhaps even the sages are part of this prophecy. The Harmonias lack power, and are the only ones who can reawaken the dragons and reclaim being the true rulers of Unova. However, people will be naturally resistant to this change, and Ghetis knew that. He knew that the only was for him to have power was through stripping the nation of it's power sources. However, his bitter heart would not be able to reawaken the dragon, so after many years, he went into the woods to discover his long lost nephew as true heir to the throne: N.
What do you think? Do you think this is plausible?