According to a GDC questionnaire that recently began circulating, the Japanese company isn't accepting Wii U game pitches from independent Japanese developers. The policy has since been confirmed by CVG.
Nintendo didn't provide its reason for excluding Japanese developers, stating only that "[t]he policy in question is the decision of Nintendo's department responsible for licensing activities in each region, and the licensing department of Nintendo is currently not accepting subject applications from individuals in Japan."
Nintendo not accepting applications from its home country is strange, especially given the recent push from console makers to create more open publishing models. Sony's PS4 will allow for self-publishing, and Microsoft has just announced that the Xbox One will support it as well.