Don't want to take this too much farther--it's a Pokémon complaint thread, after all--but Ridley's alts are references to some of his color palettes throughout the years (as well as various Space Pirate palettes). Yeah, a lot of them are jarring, but for the most part they work and get some use by somebody.
Here's my take on the lack of Shiny palettes for Smash's Pokémon reps:
Pikachu/Pichu/Jigglypuff: possibly too subtle for Smash (though the inclusion of Spiky-eared Pichu makes this a fairly weak argument).
Mewtwo: actually don't understand this one, unless the Smash devs just didn't like the bright green its actual shiny has. They included Ness (a Pokémon Trainer stand-in) sneaking up on "green" Mewtwo with a Master Ball in Mewtwo's Smash 4 DLC trailer so they're very aware that that color is the closest they have to its shiny variant.
Lucario: Aside from maybe just wanting to keep all his palettes primarily cool colors, I don't have a good reason why they wouldn't add this. Maybe they think it would clash with its Aura effects?
Charizard/Squirtle/Ivysaur: aside from losing their iconic appearances (which doesn't really make sense with all the other palettes), these should probably be in.
Greninja: its black alt is fairly close, but doesn't go all the way. I could see this being an actually weighted choice; by keeping its underbelly tan it helps make Greninja's actions clearer.
Incineroar: I personally think it actually has its shiny and saying it doesn't is splitting hairs, but w/e.
Here's my take on the lack of Shiny palettes for Smash's Pokémon reps:
Pikachu/Pichu/Jigglypuff: possibly too subtle for Smash (though the inclusion of Spiky-eared Pichu makes this a fairly weak argument).
Mewtwo: actually don't understand this one, unless the Smash devs just didn't like the bright green its actual shiny has. They included Ness (a Pokémon Trainer stand-in) sneaking up on "green" Mewtwo with a Master Ball in Mewtwo's Smash 4 DLC trailer so they're very aware that that color is the closest they have to its shiny variant.
Lucario: Aside from maybe just wanting to keep all his palettes primarily cool colors, I don't have a good reason why they wouldn't add this. Maybe they think it would clash with its Aura effects?
Charizard/Squirtle/Ivysaur: aside from losing their iconic appearances (which doesn't really make sense with all the other palettes), these should probably be in.
Greninja: its black alt is fairly close, but doesn't go all the way. I could see this being an actually weighted choice; by keeping its underbelly tan it helps make Greninja's actions clearer.
Incineroar: I personally think it actually has its shiny and saying it doesn't is splitting hairs, but w/e.