There has been numerous discussion threads on this site disputing clone characters in both melee and brawl. Neither side ever wins the argument because neither is ever willing to back down and change their opinions. It's kinda sad, really... But I digress.
Personally I disagree that Gannon's move set is a clone of falcons. While they have many similar qualities in terms of how the moves appear to look, their properties are nothing alike, an being a good player as captain falcon does not at all mean you will be remotely effective with ganondorf. They play completely different, as do their moves. In melee, Ganon and falcon, fox and falco, pikachu and pitchu, link and young link, etc, etc, those were more closely to the definition of clone characters. They remedied many of these in brawl, and will likely remedy more in the next installment.