I hate the idea that Ratatoskr is gone, but given what happens to Estinien at the end of the MSQ, I wonder if something similar can't occur with Ratatoskr. After all, according to what we've been told, most, if not all current Ishgardians/Coerthans are descended from the people who feasted on R's power. As noted in game, "just a sip" of dragon's blood is enough to awaken the latent dravanian power within them, turning them into a dragon. In a sense, this kinda makes all of these people "children" of Ratatoskr, which, if you look at it from that perspective, adds an extra layer of F'-ed up to what Nidhogg has been doing.
But it also means, if N can be reborn by essentially possessing Estinien, then does that mean R could also be reconstituted somehow? They both essentially had the same thing happen to them, only N's power was concentrated in his two eyes, while R's power is spread across likely thousands of individuals. It's probably a long shot, but I'm kind of giddy at the idea that the true end of the Dragonsong War will come only when the people of Ishgard and Coerthas find a way to "give up" the latent power of R that is in their blood, thus paving the way for R to be reborn.