There's some flaws here;
Ganondorf is all about "Power" and actually has artwork of him about to punch Link in OOT's settings. This is literally his Forward Air.
Lucina is a fair point, but she was going to be an alt anyway due to the same body shape, which is why the clone thing happens. The body shapes needs to be the same. Any clone could work as an alternate costume due to this, but aren't for many reasons(one being records only apply to different characters in their own slots, due to some programming quirk, the other is he believes different movesets justifies their own slots).
Dark Pit literally is a carbon copy of Pit physically. He can use different weapons. And he does, especially in his Final Smash. It's why he doesn't work as an alternate costume. He wouldn't be caught dead using the Three Sacred Treasures. He also uses an actual different arm and a different actual bow. Only the Orbitars are the same item, and his Up B... is just different colors. He does have differences in what he uses. Obviously this is really different in gameplay much, or sometimes at all. But what you said isn't that accurate.
Young Link does in Majora's Mask. His basic stage added is Great Bay as well. From Majora's Mask. He's still OOT-based, but it's not unfounded. However, the trophies treat him as the Link from the original Zelda game, which explains why he uses the Bow. Regular Link had the Boomerang in Smash 64 as well, as he was more a combination of multiple Links and was designed to represent their most iconic arsenal(Bow, Bomb, Arrows, Spin Attack). OOT was just his model. He's still based upon OOT, but not entirely.
Lucina is one I can agree felt like she was done wrong. But that's the only one truly it. Ganondorf wasn't going to even get in without the clone thing.
"
Ganondorf was a very lucky character [to get in].
To be honest, I had no plans to bring Ganondorf to Smash, but because of various convenient circumstances, he was able to join the fight.
(I received the model, the traits were clearly defined, the body proportions matched Captain Falcon, and above else his popularity was high.)"
https://sourcegaming.info/2016/01/11/melee-ganondorf/ Basically? He may not have gotten into Brawl either. While it's possible, if the tech demo never happened, there wouldn't be nearly as much of an outcry for him(mostly due to him being a clone). Maybe we would've gotten Toon Ganondorf instead. Maybe something else could've happened. We don't know. We just know he was lucky to get in due to being able to be a clone in the first place. His chances were pretty low beyond that.