So he is the descendant of Unova hero/king right? It was speculated that the name of the king in underwater ruins is "Harmonia". While GF flip-flop on N, Ghetsis's surname is still Harmonia. It would also explain his motive. He believed he is entitled to the poition of Unova's ruler due to his heritage.
Even in the shadow triad BW2 post-league fight they slipped that they are "royal" (as oppose to loyal) servant of Ghetsis.
I also still believed that N and Ghetsis are blood-related. And Ghetsis is the one who put infant N in the forest in the first place, to engineer his own "chosen one" with ability to talk with pokemon in order to awake the dragon.