Obito had thought he'd lost to someone like Ōtsutsuki Isshiki, an Ōtsutsuki secretly hiding in the Shinobi World. He hadn't expected that his nightmare, "A," was just a thirteen- or fourteen-year-old Uchiha boy. His shock gave way to the realization of just how wide the gap between himself and Shinji was.
So this time, he didn't hesitate. He offered up his left eye.
After taking the Mangekyō Sharingan Obito handed him, Shinji stored it in a small nutrient tank.
Obito asked, "When are you going to kill me?"
Shinji put the "A" mask back on and casually replied, "What do you think?"
In truth, given Shinji's current strength, the "A" identity had become largely unnecessary. That was why he had told Obito who he really was.
But the Overlord of Fear still posed a threat, and there was no harm in having another layer of disguise, so he put the mask back on.
Obito said, "That's right. My life or death doesn't matter to you at all."
Shinji merely waved a hand and ordered one of the Tenseigan puppets beside him to take Obito away.
Obito was right that Shinji didn't care whether he lived or died—but not entirely.
With the Overlord of Fear's threat drawing nearer and growing greater, every bit of strength in the Shinobi World gave Shinji more confidence in facing it. So he cared not only about powerful Kage Level fighters like Obito, but even ordinary Jonin and Chunin.
Because, with the Infinite Tsukuyomi at his disposal, Shinji really could, in the final moment of crisis, use it to gather all the Chakra in the Shinobi World into himself and make one last desperate stand against the Overlord of Fear.
That was why Shinji wouldn't kill Obito.
Just then, Haku and Yakumo arrived in the meeting