I managed to get the Operate Star Force save I use on my 3DS to be loaded on the Wii U and vice-versa (also OSF works perfectly on the Wii U). I had the trim down the save I pulled from the 3DS to 64K for it to load on the Wii U but luckily after that it stays at 64K no matter which system I load and save it on (so I won't have to do any future conversions to it if I pass it back to the 3DS and pick it up there).

This is cause for celebration.