Unless I'm mistaken there hasn't yet been any indication that the Paper Mario series will be treated separately from the regular Mario series...
...
I guess I shouldn't have omited that "detail".
Take a look at the mario kart stage on the 3DS. It;s one location of one instalment of a popular series. In theory, it's a different series but still a branch to the main one. In smash however, because of how the stage depicting the series only represent one place from one game, it's not enough to tell that it's a separate entity but rather a branch of the main series. It means that this series is annexed to the main one and can almost be treated as combined.
The Paper Mario stage however, doesn't follow this logic and that's because of the comparison between the 2 pictures presented. The first one shows a game from 2012 while the second one shows a game from 2004 and we still don't know if there's more. But just the pictures, it's a 8 years gap between the game repped. That's VERY broad, so much that it reps the series of at least 75%. The only game that would be omited is PM64 and SPM is implied since an older game got repped.
It's so broad that it's like he repped the series as a whole and so, is not like the mario kart stage.
In other words, it's more a separate entity than being annexed to the main series and doing the latter anyway would make the stage too "out of there" to make sense as a main series rep and so, the repping would be redundant.
That's why I think it's likely a tease.