About Robin's down special...
Sakurai said:
Although Robin doesn’t use dark magic in FE:A, I decided to assign it as his down special. It isn’t the first time I’ve given moves to a character that they don’t use in their respective game in order to capture certain aspects of the original title.
http://www.sourcegaming.info/2015/06/28/sakurais-famitsu-column-vol-457-abilities-unlike-any-other/
Zelda uses the spells Link used in Ocarina of Time, Ness and Lucas use PSI attacks from their fellow party members, and so on... People often talk about series representation and whatnot. This is a form of that. The characters may not just represent themselves, but also the games and series they come from.
And in FEA, Robin can use dark magic if re-classed to a Dark Mage.
On Ganondorf being a clone, it's pretty much because of his last-minute addition back in Melee: in fact, he was the last character added to the roster.
His model wasn't made for Melee, but was imported from the
SpaceWorld 2000 tech demo. It happened to be best suited for Captain Falcon's animations due to similar body shapes and he was added because he was a popular character at the time (and still is, being the main villain of the Zelda series and all).
Sakurai doesn't seem to like changing movesets too much between each iteration. Even if some special moves change or some animations are overhauled, the overall core concept of each character has remained the same thus far.
Plus, Sakurai receives input from the characters' creators/owners when designing the characters. This shouldn't be surprising when working with copyrighted content.
After all, Sakurai is not part of Nintendo, Sega, Capcom, Bandai Namco or any other companies that own the characters in Smash. He's an independent developer. Keep in mind that content creators can be rather protective towards their stuff, so Sakurai can't just do whatever he wants with the characters. His talk about accurate portrayals is not completely unfounded.
Also, check these out:
http://www.sourcegaming.info/2015/07/11/gdc-2008-translation/
http://www.sourcegaming.info/2015/07/09/megaman-villager-wiifit/
Sure, Sakurai does make a lot of decisions based on his whims. After all, he is the game designer. However, I don't believe his decisions are illogical. Though whether people agree or not with his decisions, that's a whole other story.
Another factor to keep in mind is how, given those are fictional characters, each individual may have different interpretations of those characters, even when most of the core concepts are understood universally.
(What does this have to do with Wolf anyway?)