It's pretty simple, as far as I can tell:
Square offers a port of Final Fantasy IX, and I and others are willing to pay $20 for it. Square offers a fully rebuilt version of Final Fantasy IV, and I and others are willing to pay $16 for it. Square offers smartphone-first Chaos Rings games, and I and others are willing to pay $10-20 each for them (and enough people must have bought it to make it worth making four of them).
FDG Mobile makes a high-quality clone of Windwaker called Oceanhorn, and I and others are willing to pay $9 for it, even without any franchise or company name recognition.'
1337 & Senri make a quirky, high quality little 2D platformer called Leo's Fortune, and I and others are wiling to pay $5 for it.
Nintendo makes a free-to-download social thing based around dressing up a Mii, and nobody messes with it for more than a week and it's largely forgotten in a couple of months.
Nintendo would very likely get $10-20 from me for an iOS Kart, or Zelda, or Mario game. Currently, they get nothing from me, because that doesn't exist, I don't own a current-gen Nintendo portable and am not going to buy one.
Clearly, if you've got big-name titles and the kind of brand goodwill Nintendo has, it's at least possible to sell quite a few copies of a familiar A-list title--even a much older entry--for prices in the $10-20 range. If you're an unknown developer with an A-list quality product, it's at least possible to sell quite a few copies for $5-10.
If Oceanhorn can be (apparently) successful just offering a Windwaker-like experience on iOS (and ATV), I'm fairly confident that Nintendo could sell a much larger number of copies of the actual Windwaker at a higher price. But so far, that's not what's happening.
I'd be happy to see Nintendo succeed at being Old Nintendo, but I'm highly skeptical the dedicated portable game system has a long-term future, so I'd be just as happy to see them become New Nintendo and succeed at that. Also, I'd kind of like to, you know, actually play their games, which isn't going to happen unless they start releasing for ATV or iOS, since I can't justify spending money on a New 3DS or Wii U for the small handful of games I'd buy.