All those moves still stay true to their characters as a whole. Mario's fireballs is a reference to his Fire Mario power, and his B-up is I guess a reference to jumping and hitting blocks with coins in them (at least that's what it seems like to me). Dedede's rocket hammer is a reference to the Masked Dedede boss fight. Him throwing Waddle Dees and stuff just show that he commands them. Zamus's moveset kinda had to be made up, since you don't ever see her fight outside of her suit in the games (could be wrong, though. I don't pay much attention to Metroid), and Ganondorf... well, nobody likes the fact that he's a clone of Falcon. Not to mention, what could you even give him? All he does in the games is throw balls of light at you, and... uses a sword... okay, so I guess they could've given him a sword to use instead of being a clone of Falcon. But still, like I said before, nobody really likes that. Oh, and also Dedede is shown as a pretty good guy in some Kirby games, too, so him being friendly in SSE isn't really straying away from his character.
Fierce Deity, on the other hand, is pretty much a different character. He has no shield, wields a two handed blade, shoots beams, and doesn't use any items. Using him as an alt for Link is like using Goron Link or Zora Link as an alt. Just because he looks like Link and uses a sword doesn't really justify an alt, in my opinion.