All of the Scion holdovers from 1.0 were problematic. It's clear that the new writers had no idea what to do with them until their reintroduction in ShB (which also changed their characterizations, see Thancred and Urianger), so they spend most of ARR through Stormblood just hovering in the background. The focus is on the new characters, Alphinaud and Alisae, and the expansion characters Aymeric/Hien/Gosetsu/etc. For Minfillia, Yda, and Papalymo, it's clear that the writers had absolutely no idea what to do with them, so those three got written out of the story so they wouldn't continue to bloat the cast with their presence. Yda even gets completely reinvented as a new character in 3.5, and then written out of the story at the end of 4.0.