How about if you weren't to change the matter of something but instead draw in other elements from something else and bind them fuse/bind them to the target? so instead of making an apple look and taste like an orange take apart the apple by the atoms, draw in the other stuff oranges have but apples lack and reconstruct and orange from the materials. The worst parts of this I can think of would be the high level of complexity within the spell/ spell circle, the possible need to gather the needed materials before hand , and the pain this would cause if you transmuted a living creature, and the possibility of a body rejecting the augmentation.



Where we saw Twilight turn a frog into an orange, it was still a frog that could still hop around and eat. Truly transmutating the frog into an orange would make it into an actual orange, but the frog would have died and would no longer exist outside of leftover material.



See any problems with this?