I am fortunate enough (so far, *knocks on wood*) to not have received this yet (**Knock on wood again**) So my thoughts go out to any of you that have had this happen to them. Hopefully this will be insightful for some of you.
** WARNING - TO ALL OF YOU WHO HAVE YOUR SAVE DATA BACKED UP AND ARE SENDING IN YOUR WII U (See italicized/bold writing Below) **
Have you backed up your save data on an external device of any sorts and sent in your WiiU for repairs?
Time to get out your pitchforks!
Nintendo restricts ALL Save Data to a single console only.
So if you send in your Wii U and they repair it/Perform a factory reset (Erase your data without backing it up themselves), then your Console ID/Encryption ID will be changed and you will not be able to transfer your save data back to your "Fixed" WiiU that they send you back.
You will lose ALL backed up saved data for EVERY game.
This is 100% Nintendo's fault because they force encrypt everything data wise, and make it only work strictly on your current console.
There have been multiple users on Reddit and other sites as well, who have backed up their save data, verified that it worked before sending in the WiiU, and then had this happen and lose ALL save data.
From all of the posts it seems that some of you believe that this is a Smash Bros U only error.
Whilst, there are a few posts saying that this has happened on past titles and Smash Bros is actually not the cause of the System Error that occurs after you format (The initial error is Smash related, but the secondary one after a factory reset is most definitely not)
In my opinion, this has something to do with Nintendo's ridiculously over-kill security for WiiU, and also making all save data linked to a single console only.
Especially when considering after this error occurs there are plenty of users reporting that they are not able to access data management, I feel that this "error" has something to do with the security in place to prevent users from modifying save files, the encryption method possibly.
Also, with as much over-kill on security as they have put on the WiiU, it wouldn't surprise me if this was in part a mix of different error codes being thrown all at once, due to the encryption method/restricted single console only save files.
It would certainly explain the data management error, as well as the System error that happens after you reformat after receiving the initial error.
TL;DR
Read Italics/Bold Above, and Nintendo's Over-Kill WiiU security in place that locks save data to a single console, on top of other security measures in place to prevent the transferring of save data by their use of extremely strict encryption methods by throwing up a flag and preventing the user from continuing unless all of these extra (un-needed mind you) security measures are in place is likely the cause.
I bet they even went so far as to write the error messages/flag checks to the system data itself, so as to completely stop people from modding/editing save files/transferring them. This would explain the whole system bricking after trying to reformat it with a "flag" already thrown up.