Okay, so, I'm going to make my bold prediction.
We're getting Wolf, OR Snake back(Less likely), and they will be released alongside Cloud.
As mentioned before, the missing stage comes before Duck Hunt on the 3ds. Now, as mentioned previously, on the WiiU version, Pirate Ship as a _f affiliated with it. All stages that share versions have this prefix to them, meaning at one point, Pirate Ship was supposed to be on the 3DS as well, but was cut, and replaced with Duck Hunt. This is why Duck Hunt is a free update, imo. However, its placeholder data was not removed for one reason or another.
With this information, this means we have 3 characters coming, and 2 stages. NOTE that the new Character AND Stage slot were added in the last patch, meaning that it's highly likely that this 3rd character could be the ballot choice, and a Newcomer to boot, since they're getting a stage alongside them.
However, this leaves the leftover data. 2 characters, and 1 stage that we already had. Cloud and Midgar are the character and stage, obviously, meaning that the other character does NOT come with a stage.
As far as Smash 4 is concerned, DLC newcomers so far always come bundled with a stage, while VETERANS do not.... See where I'm going with this?
TL;DR: If the 2nd stage on the 3DS was meant for Pirate Ship and is now just leftover data of what could have been, this almost GUARANTEES us a VETERAN reveal alongside Cloud.
Am I crazy, or am I just crazy?