I'm sure Ness will make an appearance in some form or another. Sakurai is all about bringing back classic characters, and it would seem strange for him to ditch an older, more internationally known character for newer and (possibly) less popular.
Not to mention. Ness got his name from the NES, much like how the main character for the original Mother, Ninten, got his name from the Nintendo. It doesn't get much more classic than that!