I want to share an experience I had with Nintendo trying to do something that normally they don't do: When I sold an ambassador-status Pikachu 3DSXL (having transferred it over from an old 3DS,) I contacted Nintendo for some help regarding giving my Nintendo account content away. Nintendo was willing to work with me through it all to make sure the buyer could link my old system to his account with all my games and keep my information secure. Mind you, it is a very unusual circumstance, but we did it!

It could be possible that with a situation like the controls being so hard to work that it's unplayable for you (just be professional about it, they will almost certainly lean more sympathetically if, for example, you have a personal issue such as carpal tunnel or a coordination disability that causes the controls to make the game unplayable/awkward and painful for you and it didn't offer you any way to alter the scheme to accomodate your condition - important wording, than if you just said other versions have better controls and so you were dissatisfied) then you might get a refund or eShop credit.

Nintendo probably has a strict digital returns policy because digital returns open a door wide for abuse, like people playing and completing a game and then trying to return it after having the experience, or just downloading it with intent to produce illegal copies and calling it an error. At least it's not Sony-bad, where you can accidentally download stuff for a system you don't have and not be able to return it. The sooner you contact someone, the better.

(It would be really cool if Nintendo had per-game accessibility options built into the operating system or as a free app to alter control schemes. I imagine it would make literally every player's life more comfortable. But, until people start talking, they may not dream it.)