Yeah, but WHEN the hell did he learn it? He didn't lose his snakes until his fight with Itachi, and since then, we've been watching everything he's been doing. First he got backstoried by Madara and awoke his Mangekyou. Then, he went to capture Bee. Then he brought Bee back to Akatsuki, then he was on his way to assassinate Danzou in the Leaf village when he found out Danzou was at the Summit.
So when did he have the time to obtain and sign a new contract?
I thought it was pretty obvious he was using Tsukiyomi on Danzou. They made it super obvious he was using his Mangekou by having him go wide-eyed and doing the *shiiiiing* sound.
Well, him not getting in any battles for 12 years actually seems totally believable judging by the way he was attacked the instant he left the village. He's obviously been a "behind the scenes" guy for a long time.
That said, yeah, it would suck if those eyes didn't recharge, because you can't realistically get replacements anymore. Although, granted, giving up an irreplacable eye is preferable to dying.