Let's walk through this story one more time.
The religiously controversial The Binding of Isaac was rejected from the 3DS eShop back in 2012. Co-developers Edmund McMillen and Florian Himsl were able to bring the game to Steam without issue, and last week, an updated version by Nicalis called The Binding of Isaac: Rebirth landed on PS4 and PS Vita.
But early in October, Nicalis hinted on Twitter that a Wii U version was in production. And in a new tweet from yesterday, the team seems to have come full circle and finally gone ahead with a 3DS version. See the image above? Look at the bottom right-hand corner to spot a 3DS XL with one of the game's menus displayed on it. Neither the Wii U or 3DS builds have been officially confirmed, but Nicalis wouldn't be doing all this teasing without good reason.
This news comes right after the Gamasutra interview with Nintendo of America's indie team of Damon Baker and David Warden, who explained that developers working on games with controversial content ought to have up-front conversations with Nintendo regarding the best way to move forward. It looks like whatever was preventing Binding from coming to eShop originally has been discussed at length and an agreement has been reached. All we can do now is wait for a proper announcement.