That was paralyzing gen that can be used on multiple targets at once, its completely different than Tsukiyomi. For Nagato controlling paths is like controlling rc car, Tsu would have to be used directly on him.
Thats terrbible example, becuase he wasnt fighting on his own.
They dont have to be fast, they are using their abilities very fast and thats all that matters. ->
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Preparing Amaterasu is not that fast. ->
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1. Itachi starts to gather his chakra in his right eye
2. "Naruto, hes using Amaterasu"
3. KB throws one of his swords
4. Nagato is using ST. "Shit, my body is moving on his own again!"
Pain has enough time to protect himself, considering that summoning is s/t jutsu, its instant.