There is already a Pokedex app, so now all they need is a Miiverse and eShop app. A Mii Maker app wouldn't work because Miis are tied to the console, not the Nintendo Network account. They need to make money with this endeavor, so charging $2 per app is reasonable. Digital books and movies cost more than that, so why should mobile games be cheaper?
But what Nintendo really needs to do is unify the friend lists between the Wii U and 3DS. Combining the eShop accounts is a good start, but why aren't the friends lists unified too?