Eli Cross

The Targs who lost their minds had one parent who was not a Targaryen. Aerys is the one exception but it was the maesters who poisoned him. I think that is the key. Godlike beings like the Targaryens should not mix blood with regular humans.

They Rhaes are just people who needed to get removed from Dany's path so she can become the ruler of Westeros. She is the female Aegon the Conqueror who will build back the kingdom and bring the remaining families in line.

I would guess the most stubborn will be the north because the Starks and their followers are savages who are not known for thinking straight. Daenerys is very smart and she will go about it to teach them a lesson. The Starks will betray the north like they betray everybody they ally with. The northmen will become wights and they will be the host of ice that Daenerys will burn later on.