Well, I know that Puzzle & Dragons Z will do well on the 3DS, and that's a game translated to a standalone cart from what was a "free" to play game that generates MILLIONS per day for Gungho Online.
If Nintendo can do this or something similar with their mobile games and come up with ways to make money NOT on timer-based gameplay, but options such as Amiibo purchases and stuff Nintendo fans already buy into, they won't be seen as doing anything unusual ...
It's too bad the Nintendo DS Ni no Kuni game never got localized for the US, as it's really good and an entirely different game.