Here is a list of all the Pokémon I would cut off the games forever:
-Seel, Dewgong
-Goldeen, Seaking
-Seedot, Nuzleaf, Shiftry
-Taillow, Swellow
-Surskit, Masquerain
-Plusle, Minun
-Azurill, Chingling, Budew
-Castform
-Clamperl, Huntail, Gorebyss
-Burmy, Wormadam, Mothim
-Glameow (Make Purugly part of Purrloin line)
-Chatot
-Finneon, Lumineon
-Phione, Manaphy
-Victini
-Patrat, Watchog
-Woobat, Swoobat
-Audino
-Throh, Sawk
-Gothita, Gothorita, Gothitelle
-Ducklett
-Cobalion, Terrakion, Virizion
-Tornadus, Thundurus, Landorus
-Meloetta
-Hoopa
-Volcanion
-Bunnelby, Diggersby
-Scatterbug, Spewpa, Vivillon
-Furfrou
-Spritzee, Aromatisse
-Swirlix, Slurpuff
-Current Sylveon (remake it)
-Pumpkaboo, Gourgeist
-Pikipek, Trumbeak, Toucannon
-Yungoos, Gumshoos
-Crabrawler, Crabominable
-Oricorio
-Wishiwashi
-Morelull, Shiinotic
-Bounsweet, Steenee, Tsareena
-Turtonator
-Togedemaru
-Buzzwole
-Pheromosa
-Xurkitree
-Celesteela
-Kartana
-Guzzlord
-Marshadow
-Poipole, Naganadel
-Blacephalon
-Zeraora
-Meltan
-Melmetal
-Glossifleur, Eldegoss
-Yamper, Boltund
-Cramorant
-Arrokuda, Barraskewda
-Sinistea, Polteageist
-Hatenna, Hattrem, Hatterene
-Mr. Rime
-Runerigus
-Milcery, Alcremie
-Falinks
-Sonjourner
-Eiscue
-Morpeko
-Kubfu, Urshifu
-Zarude
-Regieleki
-Regidrago
-Enamorus
-Tandemaus, Maushold
-Smoliv, Dolliv, Arboliva
-Squawkabilly
-Maschiff, Mabosstiff
-Wiglett, Wugtrio
-Bombirdier
-Palafin
-Flamigo
-Veluza
-Dondozo
-Tatsugiri
-Coldsire
And the following would be removed from player's control, and become lore/gym leader/NPC-only (effectively removed from certain games)
-All legendary and mythical Pokémon from all generations
-Wailord
-Rotom
-Type: Null
-Silvally
-Tapu Koko
-Tapu Lele
-Tapu Bulu
-Tapu Fini
-Cosmog
-Cosmoem
-Cyclizar
-All paradox Pokémon
-Koraidon, Miraidon