The Azure Dragoon plot point is pretty disappointing... We're an Azure Dragoon at the same time as Estinien! Why? Who cares! Hopefully 4.0s Job quests touch on that, seeing as we sure as hell aren't still being chosen by Nidhoggs Eye, although 10g says they just go "Hraesvlgrs Eye chose you in 3.3!" and nothing more is said...
There are a few possibilities as to why Nidhoggs eye picks us, my favorites being he never actually picked any Azure Dragoons, he just noticed them and Ishgard mistook that metaphorical crooked eyebrow to mean Nidhogg chose them... Ratatoskr, in some small sense, still being alive in Ishgard and manifesting most strongly through the Azure Dragoon would be a particularly heartbreaking scenario... Nothing backing that up though, and it doesn't explain why we're an Azure Dragoon... Midgardsormr would be my explanation there; We're destined to be connected to him, and thus an Azure Dragoon, and Nidhoggs Eye reacts to that... Kinda backed up by our Limit Break...
I think the more likely, though kinda boring explanation, is the one we've already been given, though... Nidhoggs Eye picks an Azure Dragoon, and in us it picked a second Azure Dragoon... Why? Well, because Ishgard has two Eyes... Why Nidhogg picks anyone is still kind of odd, though giving Ishgard hope is a fair explanation, but then Nidhogg tried to take control of Estinien all the same... Still, the city had two Eyes, one picked Estinien, the other picked us... Where was the other Eye? Fused to Haldrath. What did Alberic see when we battled Estinien? Haldrath... We called upon the power of "our" Eye, and manifested the armor it was fused to as a result... No explanation for why the second Eye only just picked a second Azure Dragoon, maybe Thordan disturbed Haldraths tomb earlier than we think to prepare for his summon and awoke the Eye in 2.0 or something...
Really hope 4.0 goes back and explains some of this though... I mean, it kinda has to, doesn't it? How can we be the Azure Dragoon, chosen by Nidhoggs Eye, when Nidhogg is dead and his Eyes foolishly tossed off a cliff? At the very least they need to explain why his Eyes are still giving us... What were they even giving us exactly? 1.x and 2.0 were kind of iffy on Dragoons, the Azure Dragoon seemed like the only one... 3.0 made it clear there is an entire order of them (although... Do they ever show up outside the Job quest? They're in the trailer, and occasionally get mentioned, but the only spears I saw at the Final Steps of Faith were held by statues... All the actual knights fighting there seemed to be Temple Knights...), and we don't seem all that different from them... I'm incline to think you could make Azure Dragoon nothing more than a title and remove any indication of "Chosen One" from it with little impact on the story...