God. I really hate how I just lost so much post due to an error with these forums.. I'd reply to you all independently, but going through that hassle was done once and lost.
I still feel like you guys are letting off the entire system of Ishgard and the Holy See off the hook. Heck, if the story never went "Turns out I'm actually EVIL" with the Archbishop, we probably would've gone on our merry way wiping out hands clean of the whole war with Ishgard never really seen too negatively. Keep in mind, the Holy See still lied to its people and lied about the history of the world and was totally fine with that. But... I'm sure most of Ishgard wouldn't have cared if the Holy See revealed the whole "Oh no Thordan totally killed the dragon out of a lust for power", why? Because it's not like Ishgardians are forgiving people with forgiveness for dragons and heretics in their hearts. For a 1000 years they've hated dragon kind (And anything that looks like a dragon) and are probably far to complacent to actually own up to the faults of Ishgard. There's plenty of ways to reason that an Ishgardian could come to the conclusion "Killing a great wyrm, even for power, is reasonable", such as "Well, look what happened with Nidhogg! Imagine if we didn't have both his eyes to defend ourselves!". This war has been a cycle of revenge killings for its entirety. Thordan killed Rhatotskar, so Nidhogg killed Thordan, which lead Thordan's son to pry Nidhogg's eyes from his head, which lead Nidhogg to condemn Ishgard, which leads to the constant back and forth of Ishgard killing dragon-kin (and anything looking like a dragon) and Nidhogg and his brood killing Ishgardians.
Don't act like this isn't a war for Ishgard where they raised men to hate dragons and heretics for just. Nidhogg, even if he does just use them for pawns, at least gave Ishgardians a way to redeem themselves. I mean shoot, what's Nidhogg going to do if all of Ishgard decided "Yeah, you know! Screw this place, our ancestors did some awful stuff and I don't want any association to it"? He looses the target of his rage then. Heck even Aymeric admits that with Ishgard gone Nidhogg would've just slithered back and probably not cared any more. So he's not some "Mad dog waiting to be put down", even with time perception BS, all of the problems that caused the war to begin are still there, and I don't mean Nidhogg himself. Plus, you guys gotta realize, these are nigh immortal beings, a death to them is far more significant than the death of any race of man, you'd be pretty enraged too if you and your sibling lived for thousands of years in peace only for some guy to kill your sister (Especially considering the reasons). Likewise, and this is something Estinien admits himself, Estinien is just as rage filled as Nidhogg is, and I doubt he's alone in that feeling. We can't begin to blame the dragons for their emotions, especially whenever the other side is just as emotional and hateful. Like, there's plenty of things to suggest Ishgard doesn't care just about "Nidhogg and his brood and trying to survive" but cares more for the killing of all dragons ( and mostly anyone that doesn't agree with them). So why aren't we calling for an entire disruption of Ishgard and holding them all accountable for the sins they've committed in their life? The hunting down of dragons (And things that vaguely look draconic), the persecution of heretics (and "heretics"), the issues with the lower class in Ishgard (And their bizarrely determined class system anyways). Those first two things even Hauchefant (Bless him) and Aymeric were still fine with, mind you, and they're suppose to be the Ishgardians we relate to. The Ishgardians still hold onto the eyes, act like they're just trying to "survive" (Hint, making heretics jump into ravines and slaughtering the Au Ra and Leafy Sea dragons is far from "survival"), and don't even bother to say "Well, turns out Thordan was the attacker and you guys are all technically descendants of the Knights Twelve" (Not like the last one would matter too much imho). Their ancestors may be long dead, but the sins they committed were still being upheld and supported.
Also it would seem the attacks on Ishgard proper were relatively a new thing due mainly to those magical wards Iceheart destroyed in 2.55, especially within the lifespan of Estinien, who tells you he's been able to lure Nidhogg away from Ishgard only up until recently, which was the attack on Ishgard proper right before we get there. Another thing to note, the Dragonsong doesn't make you a slave to Nidhogg if you're a dragon, otherwise Midgardsormr or Hraesvelgr would've easily been able to stop it, it really seems to be more of a call to arms that dragons can either ignore or begin to join in as well. So any idea that "Drinking Dragon's blood and awakening Rhatotskar's essence makes you a slave to Nidhogg!" isn't confirmed, they're pawns of Nidhogg by their own will until otherwise proven. And as a side personal note, I really hope Estinien-Nidhogg end up balancing each other out, allowing Nidhogg to see all the suffering he's caused thanks to Estinien, last thing I want to do after this whole shebang is kill more things.
Honestly this is also the beauty of this story, the comparison that it continues to push with those of us who we ally with and our enemies. Just as in 2.0 the Garleans and the Eorzean states mirrored each other (The suppression of the eikons/primals primarily along with plenty of other elements), 3.0 shows Ishgard and Nidhogg's brood, both groups consumed with contempt for the other, both determined to wipe the other one out for things that occurred in the past. Though, while we begin to address Ishgard's problems (Such as the whole awkward class system) it's only a step in the right direction, we've yet to deal with Eorzea's problems as well. This issue somewhat reminds me of the thread we had about the relic weapons, in which we kill thousands of beastmen for, and yet we're rewarded for it with a glowing weapon, you'll have to wonder if these sorts of things will ever actually be addressed though.