This comes from a IGN with Dan Adelman from Nintendo...

"It kind of kills me...it kills me right now that I had to make that phone call. We carve out some categories of content we don't allow. Religious themes is one of those topics. And so it was deemed to be in violation of that. Maybe we should revisit the entire concept guideline on religious themes. Maybe we should just get rid of that altogether. But given that, that's right now one of our stances."

"We're definitely open to revisiting [policies] from time to time. What we need to do is be a bit more flexible sometimes as far as interpreting those guidelines and making exceptions where they do make sense. But we're a large company. We're kind of going through some of our own growing pains in that regard."

Damon Baker, who does marketing at Nintendo, adds...

"There have been a lot of initiatives recently in terms of revamping the guidelines, re-addressing how to make the development process easy as possible for Nintendo platforms...We're going to continue to hit that message over and over. But hopefully it's becoming more and more clear that it's easier than ever before to develop games for Nintendo platforms."

Source: IGN