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I completely forgot. Was it ever explained?
I think Shin was a Shisui clone. That would explain some of the physical resemblance, his affiliation with itachi, and I think Ao said Danzo's arm has the same chakra color as Shisui. I think Kishi just rushed Shin out before he could explain some more stuff.
Shin wasn't a clone. The onion Shins were clones.
Ao was talking about Danzo's eye, which was Shisui's.
Kishi obviously changed his mind on a few things while he wrote it.
Kishi couldn't think of any other way of wanking itachi into the gaiden.