5. Elidibus' words
This one is super weird and it is 100% nothing but for some reason it really bothers me (in fact it's the whole motivation for me to write this thread, believe it or not). When Elidibus gets absorbed by the tower in the end of 5.3, he says the words "Reconciliation. Elidibus. I was needed". Why did he say his own name? I know it's not actually his name but his title, but still, why say it? Is he implying that "Elidibus" is the title given to the one who will lead the Ancients when they need for guidance? Or does the name Elidibus have another meaning for them, something that connects with "Reconciliation", perhaps?. Like I said, it's a nitpick, but there it is.
6. Future Sight
I've posted this in a thread before, but I'll briefly mention it again. In the Ivalice questline we're introduced to someone who has the ability to see the future using the Echo. As far as I know Mikoto is the only character who naturally has this ability, of course she was captured and now this ability was imbued into other Bozjan personel. Regardless, I think that being able to accurately predict the near future is an incredible skill that is never mentioned outside of that questline, and I personally think it should.
7. XIth Legion and Nagxia
The XIth legion is one of the few who has almost never been talked about. In fact, as far as I know, it is only very briefly mentioned in one of Bozja's field notes, pointing out that they brutally slaughtered an entire village in the Nagxia region. The only reason why I'm mentioning this one is because I think this plot line was supposed to be further explored in 6.0 back when it was still planned to be an Ilsabard expansion (I'm not even sure if Nagxia counts as Ilsabard or Othard, but still) and also Corvos, of course.
8. Zenos' dream
Ahhhh, this one makes me lose sleep at night. Zenos had dreams of the Final days. Dreams that were mentioned ever since patch 5.2, and were mentioned in 6.0 as well. What bothers me is Fandaniel's comment when Zenos explains to him his dream: "Could Emet-Selch have found a way...? Precious few possess memories of the Final Days." Could he have found a way to what? PLEASE tell me. I think Yoshida later said that it was due to Zenos being a descendant of Emet's and getting some of his memories because of it, but that seems like they just abandoned this plot line, because Fandaniel implies differently. Maybe this was scrapped when they changed 6.0 to not be the Ilsabard expansion?