Both the Eorzea Alliance and Garlemald Empire share the same issue of keeping the world safe from primals. Garlemald believes that they should be fought by everyone being unified and all ruled under one leader. While the Eorzea Alliance believes in joining different minds together and goes about a way that benefits everyone, not just themselves (ideally at least). Basically, Garlemald's methods are the most efficient and would be a better system of keeping things in check, but you are basically tossing your freedom away in the process, which is worse in the long run.

These two side's ideals are just too different for them to fully cooperate. The only way I can see us joining them is if by us or someone else conquers them and takes over their government, forcing them into submission. How the game sets them up however, there is always -someone- from there going to cause trouble and will likely always be each expansion pack, rather if they are the main focus or not. I think the large scale attempt to take over Eorzea from 2.0 will likely not be a thing for a good while. I see Garlemald right now as the group that will make the situation worse in another situation that is going on like in the Heavensward story.

Maybe we will get more defectors like Cid and get more of their technology like the magitek armor, but I don't see us ever allying with them.