I don't think there's anything wrong with Samus fighting without her armor when we have a fitness trainer and plant holding their own against Ganondorf or Palutena. It's not canonically logical, but Smash hardly ever makes sense within individual canons anyway.
Honestly what has Ganon done to make him seem so powerful in everyone's eyes? Killing gods? Literally half of the Smash cast have defeated "gods" at this point.
His "holy weapons" thing? Again, half of the verses have a good vs. evil thing where holy macguffins exist specifically to ward evil off. It's not out of the question for the Star Rod, Peach and her Wish/Star/Heart Magic, pretty much any important FE Sword, The Luminary, Simon/Richter, Pit and Palu, and probably way more to overcome this.
Hell, Palutena herself isn't very impressive. She has the title of. "goddess", but her best showing waa throwing an island or something like that while Pit then had to save her after she was overcome by a threat. And again, god slaying is a pretty overdone Japanese (hell, even some Western) trope at this point.
Granted, Ganondorf legitimately is solidly in the mid tiers of the Smash cast in terms of canon powers and abilities as of now, so I guess he is a good threshold.
Zelda itself is among the most powerful Nintendo verses, but only because of the Golden Godesses creating the universe along with an unintended multiverse.
Funnily enough, Pokémon is probably Nintendo's most powerful franchise due to Arceus and the Creation Trio, with the only other one that comes close to my knowledge being Paper Mario with the Pure Hearts and Chaos Heart along with Super Dimentio.
Kirby might reach those levels soon with a confirmed multiverse, but it's currently not there yet.
Fire Emblem has a multiverse as well, but it only reaches such a power level from Heroes, which is non-canon.
Mother also has a confirmed multiverse with that dragon thing being a possible threat to it.
Dragon Quest has a multiverse and multiple characters who can end it, I believe. Probably among the Top 5 and is a contender with the pokémon, but I believe it still loses out.
Then you have the verses with characters who can create/destroy universes of which there are PLENTY. At least a dozen now with the Third Parties included.
Wii Fit Trainer is probably the truly weakest. Olimar only beats her out if we trust the info on his ship that states it can destroy stars, otherwise he loses and Villager can chop tress down with a few swings, literally pluck trees out of the ground, and can fish a whale shark out of the water, so it stands to reason that based on strength, they actually edge out Wii Fit Trainer.
As for the person who said Krystal has a very fleshed out character when compared to most of the other Star Fox characters? Like, where? Her only purpose for the series was for an arbitrary romance plot with Fox along with sex appeal because she's a vixen. Even in terms of her potential in Smash, she barely does any of the fighting in her debut and actually has to be saved while the other games have her mostly taking the backseat to the other members with romance and drama being her main focal points in Command.
She would be cool in terms of the moveset, but not because of her character itself. And saying Star Wolf ain't as developed includes Wolf, which I should tell you is the wrong fight to pick when trying to argue for Krystal's inclusion. I'll agree she's the likeliest character after Falco and Wolf, and in my opinion, she should have priority over Falco, but she's not gonna have more priority and significance to the franchise than Wolf.
It's like arguing Elizabeth from The Seven Deadly Sins is a much better character than Ban. Elizabeth is integral toward the plot, but she's not nearly as significant nor as fleshed out.
Of course, this is just my opinion, though.