MSQ
While throwing the Eyes off of the Steps of Faith might seem like a boneheaded idea, I'm pretty certain we've seen the last of Nidhogg. His freakin' spirit left, after all, so even if someone were to retrieve his Eyes undamaged they'd probably be little more than aetheric batteries.

As for Haurchefant and Ysayle's spirits intervening when we were trying to pull the Eyes off of Estinien's armor, Alphinaud stops himself just short of saying he could have sworn he felt them after the fight. The Echo might just have granted us better clarity, or perhaps it's like Zack in VII: Advent Children Complete. Ehh... don't think too hard about it, yeah?


Warring Triad
Unukalhai does say, or at least heavily imply, that there are other worlds with sapient life. While this should have massive implications and open myriad possibilities, I seriously doubt many of them will be explored. If anything we're probably looking at a IX-ish setup, albeit with sentient crystals as opposed to the passive ones of that universe.

As for Unukalhai's exposition on his past... yeah. Probably "artificially" given the Echo a la the Sahagin Elder, chances are it were Elidibus. I'm still not entirely sold on the idea; I'd like to think they wouldn't make it that obvious while still keeping the whole air of mystery around the kid.