Well, I was doing a bit of research and I stumbled upon an article stating that Lucas (from Mother 3 on the GBA) was supposed to replace Ness in SSBM. This didn't happen because Mother 3's release date was delayed a few weeks after SSBM's release. And it would be kinda weird to put a character into SSBM if he hasn't even debuted yet. So they decided to keep Ness.
And seeing that Mother 3 is already out, then you can already guess what's going to happen.
Good bye Ness. We hardly knew ya.