Yeah, so Edmund McMillen has talked to the website ars technica about why Binding of Isaac was turned down for the 3ds service, and why it has not affected his relationship with Nintendo. He says that the main reason the game got turned down was religious content.
McMillen recalls Nintendo representatives he talked to making a distinction between blasphemous content (which would have been surprisingly acceptable) and overtly "religious" content that might be more sensitive. "If there's blasphemous content it's probably fine… because blasphemy is in most games… everything is blasphemous for one religion and not for another. Since demons and stuff are in games all the time, and that's considered blasphemous to some Christians, that's fine. I guess the way I talked about things in the game wasn't necessarily blasphemous, but also considered religious and something they don't want to deal with."
But, McMillen says that he knows where they were coming from on the decision and doesn't blame everyone at the company.
Despite the rejection eventually handed down by Nintendo, McMillen said the decision didn't reflect the will of everyone he'd worked with at the company. "I know for a fact there were quite a few people there really pulling for the game," he said. "I know there are a lot of people out there saying 'Eeesh, why did Nintendo do that, aren't they trying to get away from that image?' Trust me, a lot of people that work there are exactly the same way. They're saying, 'Aw fuck, we're back where we started again,' because they're trying to pull away from the image of Nintendo being only family-friendly over there and censoring games."
He also tells internet commenters to quit raging at Nintendo and "fuck off"(in McMillen fashion). Anyway as a Nintendo fan this at least gives me some hope, knowing there are people like McMillen described at the company. I just hope they get their way more often than not.