I humbly await this moment...
I'm not sure if you've played the Limsa storyline, so I'll throw this out there just in case. Y'shtola (a member of the Circle of Knowing, possibly an Archon) was primarily in Limsa Lominsa to track down "The Key," an item stolen from Seal Rock, which some to believe to be a mythical island called Swallowtail Roam; home to a mythical sea serpent (NOT Leviathan, much to my chagrin!) created by Llymlaen.
Y'shtola directly states that the Ascians are after the key, and we know that Ascian means "without shadow." She makes several inquiries as to whether people have noticed anyone around who is missing a shadow, and demands to see Emerick's "shadowless associate." Emerick was, of course, colluding with Travanchet to steal the key.
The case against him is pretty damning. But, hey, I was wrong about Leviathan and that was pretty much the only thing in all of my theories that I actually would have bet money on aside from the Dalamud = Prison thing. The Twelve are just really into creating great beasts that seem to be a lot like primals but totally aren't.
In retrospect, I guess I should have bet against it being Levaithan because that would have made him the only primal who just showed up and cleaned house without talking. The other primals just drone on and on about "Feed me aether" this and "Don't summon the others" that. All the serpent ever said was "RAAAAAAAAAAAAA." Same with Midgardsormr. No diatribes about being the only god, just "RAAAAAAAA-explodes" It's all so clear now.
NEW RULE:
From now on, it's not a primal until it gives a pretentious monologue.
(Oh sh- wait, does that mean I'm a primal?)
The gunhalberd was definitely Nael's, but you should keep in mind that Hildebrand might not exactly be 100% canon; he treads the line very carefully. Comic relief characters who tread the fourth wall like a tightripe, never falling victim to their own hilarious idiocy in any way, are somewhat of a trope. XIV took a very dark and serious turn that engulfed us in nothing but concepts like genocide and hopelessness in order to balance out the dangerless-ness of 1.X and justify the drastic changes coming for ARR. Hildebrand let us take a break from that; he was practically a mockery of our own apocalypse.
I'm sure he's going to survive much worse than an inadvertent skydive sans parachute in the future without it ever being called attention to.
As for him being at the final battle, remember also that the End of an Era cinematic was supposed to be serious and depressing. It's far more likely that in the future we'll meet up with Hildebrand, who won't even have a scratch on him, and he'll weave some wildly unbelievable and hilarious tale that lets us see the final battle through his eyes - which will again probably be a mockery of the actual events and probably not 100% canon.
(I can't wait.)
...
...
We're dead. We're all dead. They've already won.
That's it, man. Game over, man! GAME OVER! What the #### are we gonna do now!?