The Mangekyo Sharingan was not something that allowed the use of the ocular techniques in both eyes the moment it awakened. It required an opportunity—or rather, familiarity with the Mangekyo—before those techniques could be used.
As for Susanoo, the Mangekyo's universal ability, as long as both eyes were intact, it could be used as soon as the eyes awakened!
In the original story, Itachi only used Amaterasu later on, after witnessing his teammate Biwa Juzo's death...
Yei did not know whether Shisui had already awakened Kotoamatsukami, but he still intended to give Shisui a reminder.
A large part of Shisui's death in the original story was because the ability of his Mangekyo became known.
Kotoamatsukami, a genjutsu capable of silently changing another person's will—anyone would be wary of it, let alone the higher-ups who controlled the village!
Even if Shisui held not the slightest ill will toward the village and could even be called loyal, this bug-level genjutsu was simply too intimidating and terrifying!
Yei did not want Shisui to die just like that.
It was not only because Kotoamatsukami was a bug-level ability. After going through a mission together last time, his relationship with Shisui was not bad either.
"Uh, why?" Shisui asked in confusion. "Only by knowing our comrades' abilities can we make better plans during missions, can't we? Besides, as long as I'm still a Konoha ninja, I won't attack my comrades or harm the village! As long as it doesn't harm the village, any ability can be used! Isn't that what you taught me, Senior?"
Yei froze. "When did I ever tell you that?"
Shisui repeated some of the things Yei had said during their previous mission.
Yei's mouth twitched. He had merely said those things casually at the time. Who knew Shisui would interpret them