Here's my take on this whole situation:
Who do you think cleaned up after the Uchiha massacre? Most likely ANBU, which means Danzon probably has the eyes of all those fallen clan members stored somewhere set aside specifically for techniques like Izanagi so he could care less about using them up. Why else would he need Orochimaru's notes...to replace eyes lost in battle.
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His only goal right now is to stay alive. He won't use Shisui's eye for Izanagi but to get away(Body Flicker)...I mean even among the Uchiha his Sharingan abilities were special...Mind control is the perfect ability for someone like Danzou.
As far as Madara, I've heard that Madara might have lost his left eye because he used Izanagi to survive his battle with the first and I've read when Itachi said his eyes (plural) were fine. My theory is that the effect of Izanagi differs when used by someone with EMS. Maybe using Izanagi didn't render him blind but stripped him of the EMS powers in his left eye and in order for his plan to work he might need both eyes. Maybe he's trying to mold Sasuke into a little Madara :hypertobi:
One thing that's been bothering me though. If Madara is making Sasuke over use his eyes so that he goes blind and chooses to uses Itachi's eyes, why didn't him and Izuna just do a swap. They would have been the $h!t and the two of them both with EMS could have beaten Hashirama and the Uchiha Clan would be running the show right now.
I think Madara has everyone there in a Tsukuyomi just to see what the outcome would be and to get Danzou to expose his abilities. His plan is to get the whole world in an Infinite Tsukuyomi so why wouldn't he have the ability to case it on more than one person at a time right now (there has to be a significant gap in power from MS to EMS). They're still standing on the bridge like statues. Anyone think this is a possibility? or am I reaching to hard?