The trouble with this sort of thing is, many of the big revelations in EW... were only arrived at by the writing and lore teams recently and hadn't actually been planned since the beginning (for instance, the
Mothercrystal just being a non-sentient crystal, Zodiark being just an empty shell, the direct connection to the lyrics of Answers etc etc).
So I think it's probably ill-advised to go searching back through earlier parts of the game to find hints that foreshadow those plot points as they probably don't even exist, or are deliberately ambigious at best or outright retcons at worst.
I did correctly guess one thing back at the start in ARR though - that the Ascians were
Hydaelyn's original percursor civilization,
as it was just so obvious, so that revelation was hardly surprising.