The question is certainly warranted. The Binding of Isaac: Rebirth, a full remake of McMillen's game, is expected out on PlayStation 4, PS Vita and Steam sometime this year, letting folks guide a terrified pink blob of a boy through a horrific basement hell. Back before Rebirth brought co-op, a new art style, and a substantial expansion to the 2011 original, there was talk of Isaac getting a Nintendo 3DS version. In February 2012, though, talks with Nintendo broke down and the 3DS port of Isaac was scrapped because of "questionable religious content."
When Rebirth was announced in 2013, possibility of a Nintendo 3DS or even Wii U version emerged as McMillen said he was in talks with Nintendo again. As of early 2014, though, an updated Rebirth FAQ said that the game's religious themes were still causing friction with Nintendo. "We want to release on 3DS, and will if given the option," read the FAQ. "Isaac currently goes against Nintendo's publishing rules due to its religious aspects. But stuff might change, you never know."
The Binding of Isaac (Rebirth Mock-Up Art)