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I never really thought about it but did any of her students actually master transfiguration in a way that was useful or meaningful? With so many giant deadly animals you would think it could have been useful in the battle of hogwarts or just surviving hogwarts in general, but no.
Imagine teaching the same subject matter to the same people for 8 years and none of it stuck.
Huh… Come to think of it…
Transfiguration always seemed like such a specific subject compared to the others. Although, then again, there’s room for divination as well.
Also:
Well, transfiguration encompasses all aspects of "turning something into something else", not just humans and animals.
As for your questions...
I think it is established that a wizard can choose whether or not to take their clothes with them when they transform. This suggests that Movie Pettigrew would have been running naked through the Forbidden Forest at the end of PoA.
Imma go with... yes? Without more information, it's hard to say for sure. Does it make a difference if the process is quick and painless? Needlessly killing something (even painlessly) still feels wrong, but "cruel" might not be the best word for it, maybe "immoral"? I think there are some cases of animate creatures being turned into inanimate objects and back again, so perhaps this points toward some sort of other plane of existence where conciousness could exist in limbo?
Animagi keep their human consciousness when they transform, though they may acquire characteristics or abilities from their animal form. Sirius spent much of his time in Azkaban as a dog, to reduce his susceptibility to the dementors. As for how Rita Skeeters brain fit inside a beetle, don't think about it too much. It is magic, after all :)
Oh snap, really? Only read/listened to the books once, whereas the movies show mostly (only?) the kind involving at least one animate thing.
During the BoH, Hermione puts a couple of Death Eaters out of action by transfiguring a staircase into a slide, and turning the tapestry at the bottom into stone. It does seem like transfiguration would be useful enough to have come up a bit more often than it did, though.