I honestly see Amaterasu as a plot device at this point. Every time we see Amaterasu get used, it is countered by the unique ability of its target.
Sasuke -> Oral Rebirth (shows that Sasuke really had Oro's jutsus)
Bee -> Clone sub (shows just how versatile Bee was in his 1st appearance)
Ei -> V2 Speed (shows how fast he was and makes Minato look good for being "faster")
Madara -> Absorbed (showing that he still retained some abilities despite coming back to life)
Obito -> Sensing and Omyoudon (Shows the prowess of Juubi Jins)
Kaguya-> Absorbed (showing ninjutsu alone won't work on Kaguya, progenitor of chakra)
Naruto -> Kyuubi cloak (showing that cloak works as barrier, which we already knew)
It is countered every time and I think it's mainly to show the abilities of the person it is used on.