By any measure, the impending game The Binding of Isaac has a rather dark and weighty tone to it, even though the depiction is old-school and vintage in nature. That's why it got an "M" rating from the Entertainment Software Rating Board, which Nintendo usually allows on its systems, but not this one. Developer Super Meat Boy said Nintendo decided not to offer licensing for the game.
The plot is as such: players control a boy named Isaac. Isaac was killed by his mother because God told her to. Now, Isaac is cast into a network of underground dungeons, fighting off hordes of monsters along the way. It's an independent title without a lot of high-end production quality, and the fact that it got an M rating while still being a graphically inferior, 2D game says a lot about how weighty the subject matter is.
As a result, Nintendo said it will not allow the game to be released on the 3DS. Super Meat Boy co-creator Edmund McMillen said in a Twitter post, "The reasons were due to the games 'questionable religious content'." The game will still be released on the PlayStation Vita and PS3, but Nintendo, which has previously heavily endorsed independent games, will have nothing to do with it.