So you can't unlock anything from linking your 3DS version of the game to your Wii U version.
In addition, you can't change custom character sets on transferred characters, you have to do any changes on the original version and transfer it again.
Smash Bros 3DS to Wii U Custom Character Transfer (Basically this is how it works, the video description states that they can't be edited though, you really should just watch it on Youtube anyway, 60fps is [tornado fang]ing silky smooth)
So have fun getting all of the custom moves and such again. Which literally wouldn't be nearly as bad if you didn't get repeats of [parasitic bomb] you already have (Thanks I needed three more Plant Barriers and two more Fighting Suits).
I just don't see the reasoning behind this.