Honestly? to the standard casual Smash player, I don't really think it matters. They're too excited about playing as Falco/Ganon to notice/care he's a clone of Fox/CF... I know people who drastically prefer TLink to Link because he's "cute", or they just like him better for whatever reason.
Then to the competitive scene, it's pretty obvious that clones, while similar to other characters, play completely differently (except in the case of Doc, Pichu). So it never really feels like Falco = Fox or Ganon = CF, etc. This is especially true in Brawl, imo.
Also, the question breaks if the new character is a clone to an existing character, somehow.
I've seen a push on Gamefaqs mainly about how Krystal should be in instead of Falco, because Falco is a clone (not saying anybody here is saying that)... and that just confuses me because A) casuals don't really care about clones and B) competitives know that Falco plays very differently than Fox does (esp in Brawl).