My understanding is that its up to the crystal to choose,Noct's bloodline wasn't legit at first.
Plus,Noct cleansed the world at the end.So maybe he exhausted the crystal and that's the end of the scourge & conflict in that world.
What makes you say they weren't first? I've seen this idea thrown around, but haven't seen it backed up. It seems more likely to me that both Noctis and Ardyn are from the same line.