Hydaelyn and Zodiark

[Enkidoh]

Indeed, I've been partial to the same idea, particularly as watching the ending scenes to the main scenario seem to basically shout that (the dialogue the Mothercrystal states clearly hints that Zodiark, far from being 'a different side of the same coin', is in fact co-existing with her, and for the player to be mindful of him (spoilered for those just joining us):

"Hear... feel... think..."
"Warrior of Light. Beloved <son/daughter>"
"The Darkness hath fled before the unclosed brilliance of thy spirit."
"Yet it lingereth still beyond the sight of men, in forgotten corners of the world."
"In the depths of the abyss yet resideth the Dark One, watchful ever."
"Til this evil be cast out, never shall the world know aught but a passing peace."
"Yet for the present, a gentle light shineth o'er the realm of Eorzea."
"With thee at it's heart."
"From sparkling mote shall it swell to glorious sun, and all the world shall bask in it's warmth."
(The Mothercrystal then moves away, and the player's character desperately reaches out to Her)
"Blessings and joy be upon thee."
"Go forth, my child, and be as a beacon of hope for Eorzea and the lands beyond, through all the days of thy life."

Some interesting ideas were hinted at here. Not only the fact that it seems Zodiark is not actually an 'opposing state' of Hydaelyn - that he in fact seems to already exist, somewhere, and that Hyadelyn was fully aware of that... that also that whole scene indeed seemed in hindsight to be something of a "goodbye and goodluck" gesture by the Mothercrystal - that the player had completed their task and were now being left pretty much to their own devices and she she was wishing them well in whatever the future holds. It would definitely explain Her lack of appearances since then in the storyline in any event.