Ganondorf is not a clone of Captain Falcon, he is a semi clone at the very least. He has some moves from Brawl onward that make him different from the Capn', like his tilts, USmash, Fair, Jab and his Side B; plus both play very, very different. Ganondorf's current moveset takes cues from Twilight Princess, just watch the final battle against him in that game.
Anyways, I disagree, Ganondorf is fine the way he is because he has been shown to be capable in hand-to-hand combat. Yes, it's true he has used his magic blasts and a sword but there is also stuff like this that shows that the king of evil is not afraid of using his fists:
And someone said earlier that they've never seen Ganondorf do a Warlock Punch or anything similar in Zelda, right? Well just look at the beginning of his fight in Ocarina of Time where he punches the floor with a magic-charged fist:
Let no one say that Ganondorf has never used something like that in Zelda.
In Twilight Princess, he occasionally elbow charges you (similar to his FSmash) and does his Sparta Kick as well.
Behold!
The triforce of power grants it's user sheer super human strength, which he uses to break off his chains and choke the Water Sage to death (inspiration for his Side B)!
So I have to disagree and say that it's not wrong the way Ganon is portrayed in Smash. His moveset takes advantage of his pure power and shows him as the super human he is, capable of crushing his opponents with his bare hands.
Ganondorf may not be the way some people want him to be, specially because his fighting style is not consistent, but you are mistaken to call his moveset wholly inaccurate.