Just make small trios/quartets (Kanto birds, Johto beasts, Hoenn regis, Sinnoh fetuses, Unova genies and mosquiteers, Alola Tapus) availiable with small conditions roaming at the region, main legendaries (Mewtwo, legends duo, weather trio, creation trio, tao trio, life trio, cosmic trio) appear on specific places after certain events, UBs appearing at Ultra Wormholes, miscellaneous legendaries (Eon duo, Heatran, Creselia, Regigigas...) have small sidequests, and Mythical being availiable to battle only after big achievements (catch a certain amount of Pokemon or Mega Stones, have every Z-Crystal or Elemental Plate, defeat a Battle Facility, beat the main story, win every Master Rank contest...). It's not impossible and can make the games extremely addictive for completionists without having to restart the game to obtain this or that exclusive Pokemon as well as take away the need of Pokebank, but that's not how the jewish of GF think.
