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If this helps with Pokémon distribution for the fangame, I have sorted the Pokémon by set. All Pokémon from the first 3 Gens are accounted for and includes cross-gens for reference.
To clarify, Pokémon in the Multiple Sets (EN) tier are only in 1 set in Japanese or in Zangoose's case, not at all. I had to stretch a bit for Zangoose. I normally wouldn't include the POP Series into this, but Delta Zangoose is only in that set.
Lucario is there due to the fact that a lot of cards added into EX Holon Phantoms came from 2 theme decks featuring it. The 8th movie did release shortly after Mirage Forest, so I'm not too surprised.
Further clarification on the Multiple Sets tiers:
>Legend Maker & Delta Species: Magnemite, Magneton, Voltorb, Electrode
>Legend Maker & Holon Phantoms: Pikachu, Omanyte, Omastar, Kabuto, Kabutops, Aerodactyl, Wobbuffet, Lileep, Cradily, Anorith, Armaldo, Absol, Regirock, Regice, Registeel
>Legend Maker & Crystal Guardians: Seedot, Nuzleaf, Shiftry, Skitty, Delcatty, Aggron, Shuppet, Banette
>Legend Maker & Dragon Frontiers: Pinsir, Swablu, Altaria
>Delta Species & Holon Phantoms: Meowth, Persian, Mewtwo, Poochyena, Mightyena, Castform
>Delta Species & Crystal Guardians: Kyogre, Groudon
>Delta Species & Dragon Frontiers: Dratini, Dragonair, Dragonite, Larvitar, Pupitar, Tyranitar, Taillow, Swellow, Ralts, Kirlia, Gardevoir, Bagon, Shelgon, Salamence
>Holon Phantoms & Crystal Guardians: Torchic, Combusken, Blaziken, Sableye, Mawile, Electrike, Manectric, Numel, Camerupt
>Holon Phantoms & Dragon Frontiers: Horsea, Seadra, Kingdra
>Holon Phantoms & POP Series: Zangoose
>Crystal Guardians & Dragon Frontiers: Charizard
>Legend Maker, Holon Phantoms, & Crystal Guardians: Aron, Lairon
>Legend Maker, Holon Phantoms, & Dragon Frontiers: Trapinch, Vibrava, Flygon
>Delta Species, Holon Phantoms, & Dragon Frontiers: Latias, Latios, Rayquaza
>Legend Maker, Holon Phantoms, Dragon Frontiers, & POP Series: Mew
