Wait, I wrote this down somewhere from seeing a list of all the shiny Pokémon…
Charizard (trade), Blastoise (trade), Paras (Legends: Arceus, random, now Parasect), Poliwhirl (Y, hunting for another Pokémon, lost to game reset), Abra (Legends: Arceus, hunting, now Alakazam), Machop (Legends: Arceus, shiny hunting for another Pokémon), Ponyta (Legends: Arceus, shiny Ponyta side quest, now Rapidash), Cubone (Ultra Sun, hunting for another Pokémon, now Alolan Marowak), Tauros (trade), Gyarados (Y, hunting for another Pokémon, lost to game reset), Eevee (trade), Mew (trade), Sudowoodo (Scarlet, random), Skiploom (Scarlet, random), Quagsire (Ultra Wormhole), Espeon (trade, traded away), Umbreon (Scarlet, shiny hunting for another Pokémon), Murkrow (Legends: Arceus, random), Stantler (Legends: Arceus, shiny hunting), Celebi (trade, traded away), Linoone (gift from sister, lost to game reset), Silcoon (Legends: Arceus, shiny hunting, now Beautifly), Lombre (Ultra Wormhole, now Ludicolo), Nuzleaf (Ultra Wormhole, now Shiftry), Swellow (Ultra Wormhole), Kirlia (Legends: Arceus, random), Nincada (trade), Meditite (Scarlet, shiny hunting for another Pokémon), two Medicham (one Ultra Wormhole, other Scarlet, shiny hunting for another Pokémon), Altaria (Ultra Wormhole), Zangoose (trade), Latias (trade), two Prinplup (one Legends: Arceus, shiny hunting, now Empoleon, other Legends: Arceus, shiny hunting), Staraptor (trade), Bidoof (Legends: Arceus, random, now Bibarel), two Budew (Legends: Arceus, both from same Massive Mass Outbreak), Roserade (trade), Combee (Legends: Arceus, random), Buizel (Scarlet, hunting for other Pokémon), two Floatzel (one Ultra Wormhole, other Scarlet, random), Stunky (Scarlet, random, traded away), Bronzor (Legends: Arceus, random, now Bronzong), Gible (Legends: Arceus, shiny hunting), Lucario (Legends: Arceus, shiny hunting for another Pokémon, Alpha), Hippowdon (Ultra Wormhole), Drapion (Ultra Wormhole), Finneon (Legends: Arceus, shiny hunting), Abomasnow (Ultra Wormhole), Gliscor (Legends: Arceus, random), Azelf (Max Lair), Arceus (trade, traded away), Emboar (trade, traded away), Gigalith (trade), Audino (Ultra Wormhole), Crustle (Ultra Wormhole), Swanna (Ultra Wormhole), Stunfisk (Ultra Wormhole), Barbaracle (Ultra Wormhole), Heliolisk (Ultra Wormhole), Gourgeist (trade), Zygarde (mystery gift), Salandit (Scarlet, shiny hunting for another Pokémon), Tapu Bulu (trade), Hisuian Voltorb (Legends: Arceus, shiny hunting, now Hisuian Electrode), Hisuian Qwilfish (Legends: Arceus, random, now Overqwil), Toedscool (Scarlet, random), Glimmet (Scarlet, shiny hunting), Great Tusk (Scarlet, shiny hunting), Scream Tail (Scarlet, shiny hunting), Brute Bonnet (Scarlet, shiny hunting), Flutter Mane (Scarlet, shiny hunting)
It even has details :D