Nintendo should make a "spectator"-app for the Wii U.
>Connect your 3DS to your Wii U
>All your local and online battles will be "broadcasted" on the Wii U, with 1080p at 60fps, in beautiful locations.
It'd get rid of everyone's complaints and it'd be easy to make. The 3DS can already connect to the Wii U, every Pokemon already has a model that looks good even in HD and all calculations are being handled by the 3DS. The Wii U can easily handle the models, so we can have better textures and shaders and a solid framerate. Since they can distribute it on the eShop, they could sell it as a supplement app to the 3DS games and they have to spend no effort on trying to come up with minigames to justify a retail game price tag. And most importantly, since you're playing on your 3DS, you can use your pokemon, and battle with other people online, even if they don't have a Wii U.
This is "your pokemon battles on the TV" at it's core, something GameFreak wanted to do since Stadium, and now they can realize it for practically no time and effort.