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In XY every Pokémon that received stat boosts received +10, but Pikachu received +20 and were redirected to Defense and Sp. Defense.
Swampert received Damp as HA in Gen 5, the Gen that nerfed Self-Destruct and Explosion. Even in Gen 7 no changes has been made to Damp, making it totally useless.
Heliolisk, a Pokémon that depends heavily on weather, was introduced on Gen 6, the Gen that nerfed weather.
Wimpod line has two exclusive abilities, and both are the same ability with different names.
XY introduced Fairy Gem but only the Normal Gem has been available in normal gameplay.
Dhelmise, a Grass/Ghost-type Pokémon that has three STABs thanks to Steelworker, is less used than a starter with the same typing.
Lurantis and Tsareena are pure Grass-types with the same role and almost the same stats (high Attack, low Speed, and unexisting bulk), but Lurantis is completely outclassed because its stats are lower than Tsareena. The worst part is that both were introduced in the same Gen and weren't version exclusives.
No National Dex in SuMo.
Staraptor has the record of being the Pokémon with the most time in BL.
Darmanitan Zen. Is the hardest Pokémon to use: Darmanitan has High HP but 35 in both defenses, high Attack, almost non existant Sp. Attack, and decent Speed. Darmanitan Zen has its Attack and Sp. Attack swapped, high bulk but low Speed, and gains the Psychic-type for no reason. To active Zen Mode it requires to lost half of your HP or lost a moveslot using Belly Drum (which boost an offensive stat you won't use makes that any Pokémon with Play Foul ends your Darmanitan Zen)