Some of the best games come from independent developers, and Nintendo seemed to recognize this when they established Unity for Wii U and Nintendo Web Framework. Efforts were actually being made to help smaller developers out. However, Nintendo is currently not accepting registration applications from Japanese indie developers.
It's a pretty strange policy, for which Nintendo has no explanation. Here is how the news got around:
This is a questionnaire (via Kotaku) from GDC that is currently circulating across Twitter in Japan. The highlighted section notes that Nintendo is not accepting apps from Japanese indie devs at this time. I mean, you can probably be Japanese but have a studio located elsewhere, but the exclusion of Japanese studios is definitely odd.
The wording does suggest that Nintendo may begin accepting Japanese applications at some point in the future. For now, however, some Japanese developers are incredibly upset over the matter.
Indie developer Toshirou Takahashi wrote, "Why, Nintendo, is 'only Japan' excluded from individual registration?"
A developer from Studio Rice Cake tweeted, "Seeing 'No Japs' written on an international-looking website is such a terrible sight that it makes me weep."