I just thought a crazy idea for a theory. Maybe the Dragons were sworn protectors of the aether/primal seal and only knew of the location, during the war between dragons and Ishgardians the Ishgardians learned the seals location. The Empire came into Eorzea and proposed that nations join them or burn. The Archduke in exchange for being left alone told The Empire of a large power source and where to find it. The Empire agreed and Ishgard closed its gates. And hence why dragons ate more pissed then ever