Nintendo's dealing with the indie scene is always ham handed. I don't think its up to Nintendo to assign labels and make judgment calls. They're so far removed from 2nd-3rd party development its not even funny, let alone embracing anything that is outside of that.
They hate what apple has done to the market and to an extent I have to agree. But they shouldn't be worried by it unless Apple actually changes the way it pays developers (ie not chicken scratch) and encourages quality titles. I personally think the 3Ds is a blunder and going down in flames unless they make some drastic revisions but I don't think that will push people out of their hand held market.
I know when I have a choice between sitting down with some crappy iphone flash game knock off from 3 years ago, or playing Dragon Quest... I lean toward quality and great art...
It doesn't help that idiot birds CEO Peter Vesterbacka goes off about mobile being where the focus is and leading the industry in innovation, and that consoles are dying. Yea... the guy is mental.