Ness and Shulk are JRPG protagonists and their power levels are exactly as absurd as that suggests. Shulk is excluded for no apparent reason, so I'll tell you how this plays out.
The only match-ups that matter are Ness vs Kratos and Ness vs Zeus. Nobody aside from Ness on the Melee roster is even close to literal-God-tier, which Kratos and Zeus are. So while Ness is fighting one of them, the other is single-handedly defeating the entire cast of Melee. Ness finishes his fight, maybe he won, if so he gets to fight the other. And then it's over.
I think it's more interesting to take such OP characters away for a moment and look at really weird match-ups. What even is Mr. Game & Watch? How would he fare against a Big Daddy? What would Mewtwo vs Cole be like? That sounds awesome. Can I get some Samus vs Raiden? He'd probably cut her up, but it would be dope as hell. Would it be Kirby or Jigglypuff fighting Fat Princess?
You forgot Ganon, he is the reincarnation of a God, he can't be killed peroid, and can only be imprisoned by the master sword which can only be used by the hero of courage. Thus he is "God-tier", except unlike Kratos and Zeus, can't be killed.
So it would be Ganon vs Kratos, and Ness vs Zeus.