What are you talking about? Back then, all Link did in his games was flail his sword around and spam arrows and bombs. They even nailed his trademark spin slash. Kirby floated around, ate people and copied their power. What's not to represent? I mean, they had to add a lot of stuff to some of them so that they'd actually have a full moveset, but I think the only two characters that really drew a big WTF were Fox and Falcon. Falcon's entire moveset was based on a different character and for some totally inexplicable reason, Fox could go Super Saiyan. Other than that, I wouldn't say their representations were what you'd call "awful".
I struggle to see how Donkey Kong in 64 is a faithful representation of the character at all. The only thing I can identify as having been from a Donkey Kong game is the ground slap. They didn't even put in his roll until Smash 4. The same goes for Ness, who has exactly 0 of his actual attacks from Earthbound.
Mario had all sorts of interesting moves in his games, from two separate flight-inducing items in SMB3 and SMW to a litany of different attacks from the then recently-released SMRPG. Instead of making his Up B the cape or something like that, they made it another jump. Instead of having him kick a shell or even use the actual spin jump he does in SMW, they invented "Mario Cyclone" out of thin air and made it his down B.
Samus has all the grace and fluidity of a sack of moldy potatoes, opting instead to give her trademark speed and maneuverability to a character who spent 99% of his canon appearances up to that point sat in a cockpit. Her moveset seems like the result of someone who has never played Metroid went on an old geocities Super Metroid fansite, picked three of her weapons and assigned them to B moves. Except, not
really, because Metroid's Charge Beam doesn't work like the one in Smash at
all.
So now there's 4, add the two you mentioned for 6, add Luigi as a clone of Mario for 7.
As far as Link is concerned, seeing as Ocarina of Time was clearly the inspiration for the character's Smash 4 incarnation, I don't think they did an especially good job. He suffers from the same issues as Samus in that while his B-moves may very well be actual attacks from his games they're all executed in such a clunky way that he doesn't feel anything like how playing as Link in OoT feels. The stuff you can do while Z-targeting offers up several movement options they just chose not to implement. Despite having an actual backflip he does while z-targetting, they gave him the same cookie-cutter roll as everyone except Samus and Yoshi. It took until Smash 4 for Link to use his Jump attack as his Dash attack, for goodness sake.
And there is empirical proof that Link and Samus's Smash 64 movesets are awful because they are the worst characters in the game.
I'm going to bring it up to 8. 3/4 of Smash 64's cast are awful representations of what the characters actually do in their games. I have no interest in debating this.