Really if we’re supposed to get upset every time a familiar, an animal, or a magitek mecha dies it’s going to be really exhausting playing a JRPG that is about fighting things. Especially one that for 10 years had just a bunch of stereotypical adventurer shenanigans go down before any sort of deeper morality was introduced.
The nixies are not on the same level as a lot of regular creations or animals considering they were brought into existence from the combination of inanimate objects for the sake of a single task yet even Y’shtola solemnly disperses their aether after but that’s still not enough for you?
And as I said before, the fact that the writers bothered to mention that a familiar with a soul is remarkable means that it just in general does not happen. The nixies are made out of water, they are not real living beings just like how the porxies are made of clay. The creations of the Ancients at Elpis, though also woven from aether, are flesh and blood living creatures and that probably plays a part in how some end up with souls since as you say, not all do, and I’m willing to bet that an inorganic and incomplete creation has far less of a chance. IIRC, Alpha took the whole of the Omega questline and some gained life experience in order to obtain a soul. I don’t think two water sprites who existed for all of 5 minutes are in the same category.
It just feels like a really poor excuse to try to say you don’t like the Scions and don’t like how the writers treat them when there’s a million better examples to use in the game especially since the some of the ones you used in your OP are flat out incorrect and colored by your bias. There is no “shocked and appalled” reaction with the butterflies, and again, not only does Y’shtola give care to the familiars, they’re not killed and are simply returned from whence they came just like Eden’s summons and beastman primals, who no one cared at all about until this thread, just because it makes us look bad.