Board Thread:Naruto Discussions/@comment-26993711-20160319001508/@comment-734582-20160320215816

Sayian101 wrote: lol if he had enough time to activate izanagi, why not just use kamui? lol If he was aware of Itachi's powers, that means he had a 50/50 chance to guess Amaterasu or Tsukuyomi. If Genjutsu works even through kamui, it means he had to take a chance with Kamui or ensure success via Izanagi.

realistically though, he had no way to be sure of what actually was happening. All Obito saw was Sasuke's Sharingan activating. Assuming it was some sort of attack was a safe bet. Since Obito had enough Sharingan, he could activate Izanagi without it being a great loss and ensure survival or risk death attempting Kamui as it may not necessarily defend against it (say, if Genjutsu works through Kamui).

As to Obito's "secret", maybe it simply was that he wasn't truly one-eyed but in fact hid a regular sharingan behind his mask?