Discrepancy in lore (spoilers)

[Vyrerus]

An outside force of magic flying space aliens fighting the Empire to a standstill at the cost of their own millennia old leaders body is probably the worst example

Within the context of the game world it isn't. The Garleans don't know that dragons are aliens, for one thing. For another, to them Eorzea is a frontier. Not only do they struggle to combat Primals without recent technological marvels, but the amount of resources they pooled into the Agrius was substantially high. They sent it in, fully expecting it to absolutely crush all opposition and raze Eorzea mostly to the ground. Instead, it's a scrap heap in the middle of a lake.

Also, aerial superiority doesn't mean as much in this world, as it does in ours. Case in point, flying Imperial dropships bombard you during the last segment of Keeper of the Lake. Not only are these bombardments non-lethal, we can anticipate where they land more precisely than the Garleans aiming them. Without a rapid fire bombardment, their normal air units can't even touch us.

Add to this, they tried the same trick twice. They built yet another dreadnaught, being a FF Empire, they are addicted to constructing them. It has been unable to leave Azys Lla for at least 15 months by my count from battle damage sustained from fighting ONE Primal.

So Garlean Dreadnaughts are O and 2 vs. Filthy Savage Magicks/Filthy Frontier Dragons. They're about to be O and 3.

To address your points directly:

A: Doesn't matter. Cost the Empire so much that they won't willingly commit that kind of force to Eorzea ever again, until the events of Stormblood.
B. It got rid of the mainstay in their military force, allowing the Alliance to engage them on somewhat even terms until Bahamut happened.
C. That's the Dragons' cost to bear, because they acted in accordance with the pact between Middy and Hydaelyn.

[Jandor]

snip.

Dragons and primals are the reason the Empire hasn't tried to push into Eorzea again, but given we're not using either of those in our armies they provide literally zero explanation for how we're forcing them back.

Dragons didn't help us at Ala Mhigo, we didn't have a primal backing us up in Ghimlyt Dark. Eorzean forces defeated Garlean airpower on their own but we're never told how.

[Vyrerus]

Dragons and primals are the reason the Empire hasn't tried to push into Eorzea again, but given we're not using either of those in our armies they provide literally zero explanation for how we're beating them now.

Dragons didn't help us at Ala Mhigo, we didn't have a primal backing us up in Ghimlyt Dark. Eorzean forces defeated Garlean airships on their own with zero in-game explanation how.

Our powers are substantial enough that we can, and we have dedicated mages and artillery for those occasions.

Shouldn't need a lot of explanation when there's literally cutscenes of the Xaela's flying on birds and down airships with axes and magic.

A cutscene of Hien riding a Yol cutting a sky armor out of the sky with one stroke of his katana.

We also have sidequests in Stormblood where the alliance takes Magitek and trains soldiers to use it.

[Jandor]

Our powers are substantial enough that we can, and we have dedicated mages and artillery for those occasions.

Shouldn't need a lot of explanation when there's literally cutscenes of the Xaela's flying on birds and down airships with axes and magic.

A cutscene of Hien riding a Yol cutting a sky armor out of the sky with one stroke of his katana.

Powerful groups of dedicated anti-air mages backed by artillery? That sounds cool, would have been nice to ever see that.

The Xaela tribes aren't deployed in Eorzea, and they don't fight any airships. They fight a force that as far as we can see consists entirely of the much much smaller Juggernauts, those things aren't that much bigger than a Yol.

Funny you mention that Hien cutscene too, that would be the cutscene where Eorzea is yet again failing when up against Garlean air power, and yet again have to be bailed out by someone else?

Seriously, what sort of absolute morons don't expect to face aerial units when sieging a city held by a faction known for air power? What an absolute clown show of a military campaign.

[Vyrerus]

Eorzea is weak to flying types

Yeah, it would have been nice to see it directly, but just like stuff like say... Aurora class airships, we don't get to see it. Speaking of those, though, they are said to be, "mid" sized. So between assault ship and dreadnaught, and honestly, from their artwork, they basically look to be half the size of a dreadnaught. Woof. Talk about still impractical.

Though the number of times we fight aerial units or blow them out of the sky is pretty high. Like that time we blew the Garlean Assault Airship out of the sky with mere mortar style cannons in CM. Or how about in Baelsar's Wall, where we blow up about half a dozen sky armors and a dropship without breaking a sweat?

Also, in case you missed it, mages don't need to even be airborne to take out airships. While I'm sure it would help, the thaumaturge limit break calls down cosmological bodies, meteors and comets, to blow up whatever the mage targets. In gameplay it's restricted to the orange/purple targetting system. In reality, it could be used to devastating effect, particularly on large, fortress style aircraft.

As far as the scene where Hien shows up to save the day goes... you're still ignoring the EASE with which the airforce was ultimately dispatched. While I would have appreciated the alliance being intelligent and having a squad of DRGs ready to just Spineshatter Dive every Sky Armor pilot, the scene is ultimately setup to be fodder for the Doman forces and Hien to arrive like sky cavalry. To so easily brush aside the fact that a single dude on a bird with a sword can cut a technological marvel out of the sky with a single stroke is pretty dumb. Also the Eorzean contingent wasn't given the chance to fight back against the air, so sudden was Hien's arrival. It'd just be a matter of ordering the mages and cannons to stop firing on Ala Mhigo's gate, and turn their attention skyward.