And the Koopalings never use Shadow Mario, and Lucina's fighting style in Awakening is nothing like Marth's, and Alph has never flown Olimar's ship. Consistency with canon is very iffy in Smash.
That's why I said "Sure they could just say "who cares" and let him use the yo-yo ".
Yet I can explain that the koopalings use the same tools and weapons as bowser jr. because they all live together and share their tools. I don't know about Fire Emblem or Pikmin so I'm not gonna try to talk about it and make a fool of myself.
What I am saying is, Ness as a character uses abilities that aren't from him, they are from his companions, Ness never uses PK Fire or PK Starstorm, one is from Paula, the other is from Poo, same with Lucas, yet when Ness fights, he uses his bat and yo-yo, and Lucas uses his stick.
Lucas could easily just use the same bat as Ness, but they decided to change that because it wasn't his weapon, instead they give him the stick and the snake rope from Duster.
What I'm saying is that, they could just let Ninten be exactly like Ness, but they Yo-yo is the most iconic attack of Ness to the point that the Kirby ability of yo-yo is a direct reference of Ness, is not just a minor detail or a minor ability, is what makes Ness himself and what differences Ninten from Ness.