I don't think anyone at Nintendo cares for Devil's Third. That has been quite apparent for a year now. The announcement of it at last year's E3 was very low-key and they didn't even try to hype it up. Since then, Nintendo has done its best to ignore the existence of the title as much as possible. Most of the marketing so far has been done by Itagaki on Facebook, lol.
Heck, when I talked to NoE's PR last year, he was happy to talk about everything they've shown at E3. With the exception of D3, which was just met with "I don't have anything to say about that".
I don't know what happened behind the scenes, but I don't think that Nintendo is particularly happy with the title. And, of course, its sales potential is absoluetly terrible. I actually feel bad for the people designing the multiplayer, since I can't imagine that it'll be alive for longer than a month.