Do you think that the Twelve will eventually become major players in the plot?

[Alberel]

You think you are joking, but it could be true. For starters we don't have much evidence wether it was really Halone who appeared (if anything appeared at all). And second, Lahabrea and co are playing a pretty long con, so it is reasonable to assume that they had a hand in planting a nation state at the doorstep of the dravanian horde. It's not like the two are waging an eternal war or anything.

Regardless of whether it was truly Halone that appeared to the Coerthans before the founding of Ishgard there has to be some true origin to the mythology of the Twelve. It is very likely the Ascians have used the myths to manipulate people since the Twelve departed Eorzea but I find it unlikely that they fabricated the very source of the mythology.

The game is full of hints and nods to the concept that every myth has a shred of truth in its origins. Something of the Twelve is real, whether they're just people, gods, or something else. Bahamut, Shiva and Phoenix are proof enough of this, and Belias' presence in the SMN quest series suggests much the same for Ifrit.