Aesthetic variations
Gender variations
Butterfree-Females have a pinkish tint to their wings
Beedrill-Males have a larger stinger
Machamp-Females have a different color to their belt
Kingler-Females have a smaller claw
Marowak-Females have a larger club
Ledyba line-Female eyes are a shinier color
Chinchou line-Males are quite smaller
Stantler-Males have larger antlers
Donphan-Females have smaller horns
Tyranitar-Females are larger
Hariyama-Females have a larger skirt
Aggron-Male horns are larger
Zangoose-Males have a bigger scar
Lucario-Females have longer "hair"
Heatran-Females have their head horns curled
Sawsbuck-Females have smaller "antlers"
Adapting variations in the anime
Pink Butterfee-Like AZ's Floette, this Pokemon has a higher BST than normal. It is always female, and has the ability Cute Charm. Though it does not have a legal shiny, hacking it reveals that everything but the pink is shinied
Crystal Onix-It has the same BST boost as AZ's Floette. The Crystal Onix has an unchanged ability, cannot evolve, and is changed to learn some Water moves. It has an ability known as Crystal Body. Crystal Body "makes this Pokemon fit for water." As such, it has a 4x resistance to Water, and 2x weakness to Fire. Its signature move, Crystal Tail, is a counterpart to Iron Tail that is also part Water
Purple Kecleon-A gift sent out whenever a Mystery Dungeon is released. This Kecleon is stronger than normal Kecleon, and has Protean as an ability
Golden Sudowoodo-Another gift. Using the "Gold Coat" to wear on Sudowoodo, it gains the Ability Water Absorb
Arctic Snorlax-A one-of-a-kind snow-based Snorlax. It is rare for possessing the Ice type, though its ability is unchanged
Pink paint-You can go to someone and paint certain Pokemon pink(their shiny will be blue instead)
Movie Pokemon
M1 Mewtwo
OT-Giovanni
Level-70
Item-Enigma Berry
Attacks-Shadow Ball, Psychic, Gastro Acid, Recover
M2 Lugia
Level-50
Item-Silver Berry(a unique berry that helps resist against Fire, Ice and Electric moves)
Attacks-Unchanged. It has Sunny Day
M3 Entei
OT-Hale
Level-100
Ability-Flash Fire
Attacks-Wish, Sacred Fire, Hidden Power, Power Gem
M4 Celebi
OT-Samuel
Level-40
Ability-It's new Hidden Ability, Immunity
Attacks-Its signature move Time Travel, Frenzy Plant, Refresh, Safeguard
M5 Latias and Latios
OT-Bianca
Level-30 and 50
Item-Soul Dew
Ability-Its Hidden Ability, Illusion
Attacks-Unchanged
M6 Jirachi
OT-Max
Level-40
Item-Liechi Berry
Ability-Unchanged
Attacks-Precipice Blades, Doom Desire and two other moves
Shinies
Winona's shiny Swellow-In the DLC, Winona's final battle involves her prize Pokemon, a shiny Swellow
Korrina's shiny Hawlucha-Referencing the anime, Pokemon WZ has you face Korrina in a rematch. She brings out her prize partner, a shiny Hawlucha
Steven's Metagross-You get to face Steven in a battle in WZ, where he has summoned his silver Metagross
Shiny Smeargle-In Artisan Cave in the Battle Fronteir of Gen 6, there in lies a Shiny Smeargle at Level 65
Random shinies-At least one trainer in each new game uses a shiny, as an easter egg to introduce you to the concept.
Non-Pokemon enemies
WZ's Lysandre: Now immortal and out of his gourd, Lysandre does something desperate. He has fused the power of the Ultimate Weapon into him, after it comes apparent his Pokemon cannot beat you. One with that Weapon of Destruction, Lysandre becomes a god-like being and attacks
Lysandre has a stat total of 700, and the ability Ultimate Aura. This Ultimate Aura prevents Mega Evolution, except the power of Zygarde. He has high HP. His typing is Dark/Fire. His attacks are Light of Ruin, King's Shield, Oblivion Wing and Geomancy. Be afraid
Cyrus: With Cyrus, he is smart enough to know you will try and catch Giratina. He has control over Giratina and its Primal state. So he uses his Red Chain powers to absorb Giratina and become a hybrid. In this state, Cyrus has the full powers of the true
Restored Forme
Restored Forme is a new forme achievable. Thanks to study of the Primal Legends, they have discovered a way to bring old Pokemon back to their original state. The key item "Primordial Key", when active, brings certain Pokemon to their original, intended state
When done on a fossil Pokemon, they will change their Rock type, gained due to fossilization, to their original typing. In addition, they will forget their Rock type moves and be able to learn moves of their original typing and vice versa, in a more extreme variation of Rotom. This effect cannot be achieved in-battle.
Non-fossil Pokemon may change typing, though nothing is certain
Both can re-arrange stats. Some small like Omastar, some large like Cofagrigus
Restored Omanyte/Omastar
Type-Ground/Water
Ability-Heavy Armor(an inverse of Weak Armor)
Restored Kabuto/Kabutops
Type-Bug/Water
Ability-Unchanged
Restored Aerodactyl/Mega Aerodactyl
Type-Dragon/Flying
Ability-Intimidate(Normal Aerodactyl)/Tough Claws(Mega Aerodactyl)
Restored Lileep/Cradily
Type-Water/Grass
Ability-Suction Cups
Restored Anorith/Armaldo
Type-Water/Bug
Ability-Compound Eyes
Restored Cranidos/Rampardos
Type-Fighting
Ability-Rock Head
Restored Shieldon/Bastiodon
Type-Normal/Steel
Ability-Fortress(this Pokemon is immune to Fighting attacks)
Restored Tirtouga/Carracosta
Type-Water/Ground
Ability-Unchanged
Restored Archen/Archeops
Type-Dragon/Flying
Ability-Aerilate
Restored Amaru/Aurorus
Type-Electric/Ice
Ability-Unchanged
Restored Tyrunt/Tyrantrum
Type-Dark/Dragon
Ability-Unchanged
Restored Claydol
Type-Ground/Psychic
Ability-Rapid Spinner(entry hazards fade when this Pokemon is sent out)
Restored Regirock(note: will not restore until Regigigas is in the Pokedex)
Type-Rock
Ability-Body Builder(This Pokemon is healed when attacked by moves of its own type)
Restored Regice(note: will not restore until Regigigas is in the Pokedex)
Type-Ice
Ability-Permafrost(Fire moves have no effect on this Pokemon)
Restored Registeel(note: will not restore until Regigigas is in the Pokedex)
Type-Steel
Ability-Fortress
Restored Yanmega
Type-Bug/Dragon
Ability-Unchanged
Restored Uxie(note: will not restore unless you have caught one of the Lake trio)
Type-Psychic/Fairy
Ability-No Guard
Restored Azelf(note: will not restore unless you have caught one of the Lake trio)
Type-Psychic/Fairy
Ability-Inner Focus
Restored Mesprit(note: will not restore unless you have caught one of the Lake trio)
Type-Psychic/Fairy
Ability-Clear Body
Restored Regigigas(note: will not restore unless you have caught Regirock, Regice and Registeel. Not allowed in the Battle Maison or Frontier)
Type-Normal/Fighting
Ability-Sweet Dreams(heals 1/8th of max HP asleep)
Restored Heatran(note: Not allowed in the Battle Frontier or Maison)
Type-Fire/Steel
Ability-Burning Body(physical and special moves used by this Pokemon have a chance of burning)
Restored Cofagrigus(note: requires max friendship)
Type-Ghost/Normal
Ability-Speed Boost
Restored Elegym/Beheeyem(note: ancient aliens reference)
Type-Psychic/Electric
Ability-Levitate
Restored Golett/Golurk
Type-Ground/Fighting
Ability-Fighting Spirit(Normal and Ghost moves are Fighting type)
Primal Legendaries
Primal Mew: After learning Light of Ruin from AZ, Mew is capable of Primal evolving on its own. It assimilates life energy from other Pokemon, in order to achieve its maximum potential. It is Psychic/Normal with Protean. Mew itself was used to be part of the Ultimate Weapon long ago
Transcendant Tower: An important aspect of the creation trio in the Gen IV remakes. It is revealed that, much like the weather trio, the creation trio has a greater power. Their current form, instead of being their natural state, is a weakened state they put themselves into as they gave much of their own essence into the creation of the universe. So the opposite process of Primal Devolution. Transcendant Revolution has the same boost as Primals and Megas, activates immediately like a Primal but can only have one on the team like a Mega
Transcendant Dialga: Dialga reveals that it sacrificed much of its power in order to keep time flowing. Transcendant Dialga is identical to Primal Pokemon. Wielding the Adamant Core, Dialga manages to fuse with time itself, becoming Transcendant Dialga. Its has 780 BST, and possesses the ability Speed Boost
Transcendant Palkia: Palkia reveals that it sacrificed much of its own power in order to keep space expanding. Trabscendant Palkia, wielding the Lustrous Core, fuses with space itself. It has 780 BST, and possesses the ability No Guard
Transcendant Giratina: Giratina lost much of its power as punishment. Cyrus manages to reel back the dimensional veil and obtains its true power. His Griseous Core allows him to prevent devestation. It has 780 BST, loses its Ghost type and gains an ability similar to Inverse Battles
Transcendant Arceus: Arceus is unique in that it does not need an item to go Transcendant. It simply need to learn to move Deific Ascent. A move with the power of Dragon Ascent, a Normal type and can hit any Pokemon with neutral damage. Even affecting Ghost Pokemon, and doing x1 damage to Steel and Rock Pokemon. Transcendant Arceus knows the ability Mastery, where every move gets STAB. It is the most powerful Pokemon to date
Primal Gensect: It is revealed that they weren't able to truly resurrect the creature Genesect came from. The Plasma Orb uses a CPU in it to analyze the original genetic structure of Genesect. It requires the three tao trio. It absorbs the ancient power within them, while holding
Primal bird trio and Lugia: Millennia ago, there was an ancient culture known as Pokelantis. They fed enormous qualities of life energy to enhance their god, Lugia. Lugia's booming energy also gave the potential for the bird trio to become as powerful as Lugia. However, the rage of Lugia and its disgust of this culture's mass sacrifice led to the destruction of their civilization(before you say too dark, compare it to AZ's backstory).
In the present, you can discover the Silver Orb, the Arctic Orb, the Zap Orb and Molten Orb. Through them, Lugia and co can safely unlock the power given to them, knowing you are trustworthy of their true might
Primal Articuno
Type-Ice/Flying
Ability-Snow Warning
Item-Artic Orb
Primal Zapdos
Type-Electric/Flying
Ability-Drizzle
Item-Zap Orb
Primal Moltres
Type-Fire/Flying
Ability-Drought
Item-Molten Orb
Primal Lugia
Type-Psychic/Dragon
Ability-Air Lock
Item-Silver Orb