Sakurai clearly didn't want to scrap and redesign a character who has fought this way for 3 games already, no matter how justified a rework would be.
Mario doesn't use powerups in his moveset. He doesn't use the cape or Racoon tail to recover, he doesn't shoot ice balls, he doesn't use the tanooki tail to attack foes, etc. This is because he was designed with the n64 in mind, and also with Smash's mechanics in mind. It's the same for MANY characters in Smash. Megaman is a product of a more modern and deliberately-nostalgic character design, and thus has more of his in-game moves in his smash moveset. He breaks a lot of conventions, but he would not be unique if there weren't those conventions in place.
Sakurai decided that projectiles belong as specials, not normals - Samus having all of her projectiles as normal attacks would make megaman (and villager) less of the unique characters they are supposed to be. Agree or disagree.
The way Samus fights is wholly unique and something you can't just throw away, even if a more Samus-y Samus would make sense. If she had ice beam and other stuff as part of her A-attack moveset in smash 64, she'd be way too projectile focused for that game. It wasn't until Megaman/Villager/etc that having projectiles as part of your normal moveset was normal. But updating Samus to fit in with this design change wouldn't work, as she already has her own established moveset.
One could also justify that there's no reason why Samus doesn't use more melee combat in her own games, wearing a suit of armor and all. Thus her Smash moveset is arguably just 'different', but not 'wrong'. Yeah, she doesn't have superspeed or roll crawl or ice beams or anything, but she still feels like a powersuit fighter with strong projectile game.
Plus, there's way more from her own games in her moveset than other characters have from their own games. Heck, it wasn't until Smash 4 that DK got the only actual attack he had in his Donkey Kong Country games - his dash attack roll. The rest of him is pretty much made up by Sakurai.
She's just a unique take on the character. Like it or not, Sakurai wasn't ready to toss the unique envisioning of Samus in the trash just to make her use ice beam and such.
I meant more like how her Beam customs are just a property change and a random custom - the Melee shot things. Why couldn't she have an Ice Beam custom, a Ice Missile custom, or a something rather than property changes? Some characters have awesome customs that reference their games like how Sonic has that one fire roll from Sonic Adventure 2?, but others just have property changes when it should be more different like Link not having his Ice Arrows, a Great Spin Attack, or a walking bomb from Twilight Princess.
However, Ice Missiles could work as a special that only freezes people after say, 60%, but otherwise functions the same as regular missiles. Like her Super Missile, she could have Power Bombs as a "power" Down Special.
I will stand by that Morph Ball should be a crawl and it's not like it changes a huge part of her like making her Up Smash into a wheel kick or making her Jab into her shooting.
I never said anything was wrong about her move set. It's just there's things should have been like customs making use of her arsenal in Metroid or Morph Ball not being her crawl. Samus primarily uses ranged weapons, but as Other M showed, she's dangerous up close as well.
Captain Falcon's move set was entirely made up, but it still flows with his characteristics of being a fast racer, his Falcon symbolism, and how a muscular, athletic, and bounty hunter guy like him would be capable of martial art feats.
Meanwhile, Ganondorf's sword victory poses lead people to believe he was conceptualized as a swordsman, but was made into a clone due to time constraints. That's one character that I argue could get an overhaul even if it's slight like making more moves like in Zelda such as Down Smash being a fist slam which might already be in place with his Fair, giving him Dead Man's Volley for his neutral Special, Side Smash being Warlock Punch, or something like making more of his moves look less like Captain Falcon's like making his Bair look a bit different, but functionally similar. Drastically, he could be a swordsman which people want because of those leftovers. If they never showed up, I don't think people would be this upset because there would no "evidence" of him using a sword. Warlock Blade even angers people since some feel it's like a big middle finger to them.
Ganondorf is a powerful, hand-to-hand combatant that nobody is like. The only "equivalent" would be Bowser, but Bowser's like a wrestler now who's fast on his feet, but slow and powerful with his attacks while Ganondorf's attacks tend to come out quick and powerful. Then you add people saying, well, Ganondorf's a speed demon in Twilight Princess. Well, if he was like that, then he'd be a broken character who makes Little Macs on For Glory looks like wimps. Imagine a bullet train about to hit you, that's what Ganondorf would be if he could move like that. Well, he's not, he's more like a regular train about to hit you.