That's why i have a Wii U Pro Controller and Wii Classic Controllers (which are much better options, except maybe for Smash) and the GC-Wii U adapter if it's necessary (not expensive, even if it is the original). No need to clutter just for ports.Except you will lose the ability to use GC controllers with supporting Wii and VC games, also from what I heard EmuNAND is pretty buggy on Wii U while as it works just fine on Wii.
Anyway, Nintendont is currently doing great, i wonder if there are still games that have problems with it.