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Autism and boredom hit, so this is a mini guide to which pokemon you can't use in the main story of their debuting generation. Trading is considered fair game, therefore version exclusives aren't gonna be considered. The level threshold is the final boss' highest leveled pokemon.
>Gen 1: 1 pokemon is post game exclusive in mewtwo (dragonite is somewhat unreasonable level wise as well but blue's highest is level 65 so fair game)
>gen 2: 12 in GS and 11 in crystal: the houndour line, larvitar line, misdreavus, sneasel (GS), lugia (GC), ho-oh (S), porygon-2 (up-grade is located in kanto), slugma line, murkrow.
>gen 3: 6 in Ruby and Sapphire, 7 in emerald: The beldum line, latios and latias, rayquaza (RS), groudon and kyogre (E). Special mention to salamence barely scraping in (evolves at level 50).
>gen 4: 7 in diamond and pearl, 5 in platinum: Dusknoir (DP), Rhyperior (DP), Porygon-Z (DP), heatran, regigigas, giratina (DP), dialga and palkia (Pt), Cresselia.
>gen 5: 6 in BW, 9 in BW2: Landorus, kyurem, reshiram/zekrom (BW2), zorua and zoroark (BW), the gollet line (BW2), hydreigon, volcarona (BW), durant (BW2), heatmor (BW2), stunfisk (BW2), cryogonal (BW2). Honorable mention to mienshao (evolves at level 50, very late game in BW), bisharp (level 52), braviary and mandibuzz in BW ( level 54, ghetsis' hydreigon's level).
>gen 6: 1 pokemon in zygarde.
>gen 7:16 in SM, 18 in USUM. Type:Null and silvally, cosmog and cosmoem, necrozma, all 4 tapus, all ultra beasts sans poipole (7 in SM, 9 in USUM). I also feel i must mention how in SM charjabug only evolves on the fouth island, what were they thinking.
>gen 8: zacian/zamazenta (sword or shield).
There's some more nuance to be had considering version exclusives but those aren't that hard to look up.
