So, some updates to the Dragonsong speculation, based on level 55 quests, so spoilered:
So, according to Hraesvelgr, his sister Ratatoskr was slain by a traitorous King Thordan, who then consumed her eye. I think this answers the lines about treachery, and the empty throne. Also, Hraesvelgr mentioned that the dragons experience the past the same way they experience the present, explaining why Nidhogg, who was first to discover the betrayal, is still enraged a thousand years later.
Correction, the Aery final scene shows that the empty throne would be Ishgard, after Haldrath refused to take the throne.