My personal theory is that they wanted to remove all those rather "weak" 1.0 characters from the story to add some of their own. Not including Moenbryda, all the characters that left us - Minfilia, Papalymo and Yda - were more stereotypes than "real" characters. Or at least that was always my impression of them - I never felt a connection to any of those 3 because there is nothing to feel connected to. They have very little character, no personal struggle, that I could have really cared about. The first time I cared about Yda was when she revealed that she was indeed Lyse and didnt want to uphold that masquared any longer.

If my theory is correct, I dont blame anyone for writing an end for those characters (which also serves as an "We're really at war and need to make sacrfices!")

With that in mind:
I can only see Thancred go, if anyone. They've invested in his character-development, at least a little, and he matured from the stereotypical Cassanova he was presetend to me in ARR.

Y'shtola is our postergirl, I'm not sure if they would retire her.

I obviously have no proof for my theory, but following that I wouldnt use the "physical weakness" that Thancred and Y'shtola are showing as argument for them to leave/die - quite the contrarary, actually! They got those weak points as character traits to make them more intresting and give them problems to deal with (up to you to decide for yourself if that worked or not...)

I think most of the characters we have now, are far better and more intresting than 2.0 Yda, Papalymo and yes, Minfilia. So if someone gets killed off, it would be more like Haurchefaunt - someone we have an emotional connection to.
Y'shtola is probably safe, thanks to being the face of FFXIV.
Thancred... at least I can say that I would need a lot more screentime with him before I would really care about his death.
A more likely candidat for me would be either Alphinaud or Alisae - we've traveled quite a bit with both them, got to know them and added bonus: If only one of the twins dies, we get to see the pain of the other one. Okay, that came out wrong... my point is: either of those deaths would be far more emotional than Thancred.

Bottomline:
I believe the old Scions needed to make room for new, more original characters and thats why they died/left. Now that they're out of the picture we'll see only/more "emotional-meanigful" deaths (if we see any).