Most of what you question is practicly simple to answer:
The writer simply had no plan.

I only heared it from second hand. But someone should had a interview, where the dev stated, that they had no idea, who the ascians was, until they had written SHB.
At the start was they only created to be the bad guys. And they had probably the idea of Zodiak as the counterpart of Hydaelin. But there whole background wasnt there. They simply set up threads and seed here and there, and looked, how the things evolved.
Similary thing will probably happen now in 7.0 and onward.

1) Dark crystal:
That was very likely Zodiak at that point. They simply had probably no designs for him and Hydaelin at that point.

2) Minfilia:
They probably maked her running back, to take her out of the picture. Because they had probably no plans for her at that point. And came than at the idea, to create her as a Oracle of light, to let Hydaelin speak with the others, when they came to her.
It is hard to tell, how much she had planed that in-universe. Because, she couldnt probably had knowed, that the others was coming (i forgot, why they came to her, i think, because of the Warrior of Darkness),

3) Zenos:
He was simply stronger as the WoL.
Until that point, had the WoL allways help.
He was in a group, when he fighted Ultima. Hydaelin protected him again Ultima spell and i think, after the rework, was Hydaelin helping him by the fight again Lahabreha directly.
Im not remembering, ih the WoL was alone again the Church leader. But the WoL had a power boost, when he fighted Nidhoog (in form of the dragon eye -as a Dragoon, do i want the exes of the other high dragons to^^).

Zenos was the first or second very powerfull enemie, the WoL had to fight completly alone (not sure, how much of trouble the underling from Gaius is now, after the rework of the coast fight). Again someone, who did nothing as to hunt powerfull enemie his whole life (Why did Zenos didnt became a Viper, the job description fit Zenos perfectly^^).
Its even more questionable, how the WoL was able to beat Zenos at the end (ok, he was again not alone). The WoL didnt had a power up, as much as i remember.

6) Future sight:
It was allready stated very early, that the power, that the WoL and others had, has differently effects.
Ours is the past vision. Future sights is logical, as a other power.
The reason, that isnt used more is probably, becvause the power is similary uncontrollable (the WoL was mostly of times not able to control his power, until Venat). Because of that is it very likely, that the people dont want to pet on that.
In addition have the writers probably not found a way, to use her more.