Well, judging by the events of B2W2...
I'm certain, judging just by the kind of person Ghetsis is, that he would probably rule Unova, and thus N would be blinded by the throne of "king" that Ghetsis would give him, Ghetsis would also be in control in the background as well. Another possible scenario is that Ghetsis would step his "son" out of control, and thus he would be ruler.
N, however, is a different matter. N would be deadbeat convinced that he was the Hero, and free all the Pokemon. Truthfully, judging how cruel Ghetsis was, Ghetsis would probably cause an "accident" and seize the throne. In the second scenario when I was talking about Ghetsis, N would probably join with Hilda/Hilbert to overthrow him. Or, another possible solution is N noticing the errors of his ways because Hilda's/Hilbert's Pokemon were glad to be battling alongside their trainers, and THEN resulting in the fight with Ghetsis.
I find it funny, though, that I lost to Ghetsis the first time, and instead of going off to rule the world, he stayed in the same place, and I was actually able to come back and try to win again. We all know that this is because they [the developers] wanted the players to be able to have a second chance, but it still seems moderately interesting to me.