Those massive airship also require a lot of resources to move around. It's why we created that wall in the burn and why taking back Rabanastre is so important - they need a lot of ceruleum to function and we're basically cutting the provision lines.
In eorzea, we never had all empire divisions against us, but a couple of them at the time, that's why the united forces of the city states, and now ishgard and doma, managed to fend them off.
Also the empire is more fighting between themselves in a civil war that fightning eorzea