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I dont know how I missed it before but this is another one of those spells, like ecstatic seizures and dwellers below, that targets an entire unit and drops the models dead with no saves. It seems to me that this spell is almost as nasty as dwellers against high strength enemies, particularly when you factor in the easier casting and the stupidity tests.
Any thoughts on this?

It's a nasty spell in a not so excellent lore that few armies have access to(and those few will more often than not pick Life instead).

It's the sucky topper to a sucky lore.

Im not sure I see what's sucky about lore of metal. The sig spell doesnt work so well against lightly armored troops but a magic missile isnt really all that effective against light infantry (which tend to come in large numbers) anyhow. Every other spell seems underwhelming but easy to cast. Seems like an effective way to keep a level 2 from blowing his own head off and consistently aiding the army, as opposed to throwing as many dice as i can get a purple sun and hoping nothing goes wrong.

I think lore of metal is just Meh. Given that other lores (Death, Shadow, Life) are ZOMGWTFHAX, nobody wants to take a lore that's meh.

The advantage of Final Transmutation is that it works on everybody, including high-strength troops like shrine-buffed chosen (given the double-shrine favor cheese, this is an important point as it's basically the only way to kill them.) It's not tied to stats.

The disadvantage is that it doesn't work as well on characters, needing a 6 to poof them. However, as many have said, the real problem with FT is the rest of the lore. Hounds is useless, the signature is useless except for killing hydras, and the armor save nerfs are very situational at best. Unless you can know the whole lore, other lores are better, and if you can know the whole lore, you are probably a slann who took life.