It might be helpful if folks posted the versions they have of stuff. Especially those who are experiencing the issue, in case there is a common thread. For me, so far I have NOT had the issue, but I am getting paranoid with all these reports. My details:
*The Wind Waker edition of the Wii U
*Hardcopy version of Smash Wii U
*No SD card in the system
*I have saved a few custom stages, characters, and Miis (in case this winds up being relevant)
*Frequent For Glory play (my most played mode, although I have played all offline modes at one time or another)
*I always back up to the title screen before shutting down. In light of the current paranoia, now I am both going back to the title screen, waiting a few seconds, and then using the Home button to return to Wii menu.