This is were I predict stuff for the Pokémon Adventures Manga.

Black 2 & White 2 chapter

Main Characters

Blake


Oshawott → Dewott → Samurott♂	Will evolve in a battle with Colress or Zinzolin. Ability: Torrent Possible new moves: Fury Cutter Water Pulse Revenge Swords Dance False Swipe Brine
Genesect	Will get controlled again by Ghetsis. Ability: Download Possible new moves: Signal Beam Magnet Bomb Zap Cannon Lock-On Screech Tri Attack Flash Cannon
Keldemaru	Will rescue and go back to the Swords of Justice after Team Plasma's defeat. Ability: Justified Possible new moves: Secret Sword Double Kick Surf Aqua Tail Retaliate Swords Dance Quick Guard
Kabutomaru♂	Ability: Battle Armor Possible new moves:
Liomaru♂	Ability: Hyper Cutter Possible new moves:
Bisharp♀	Will be caught so Blake has more power against Team Plasma. Ability: Defiant Possible moves:
Probopass♂	I can see Probopass using Magnet Pull to take back stuff like the DNA Splicers. Ability: Magnet Pull Possible moves:

Whitley


Foongy♂	Is forced to evolve for a Pokéstar Studios movie or something else. Ability: Effect Spore Possible new moves: Synthesis Seed Bomb Energy Ball Poison Powder Worry Seed Sludge Bomb
Cubchoo♀	Whi-Two may catch this because it's SO CUTE!!!!! Ability: Snow Cloak Possible moves:
Riolu♂	Pokéstar Studios needs one so Whi-Two will catch it for them. Ability: Steadfast Possible moves:
Spoink → Grumpig♀	Caught at Reversal Mountain. Ability: Own Tempo Possible moves:
Zorua♀	Given by Rood. Ability: Illusion Possible new moves:
Maractus♀	It will be caught at Route 4. Ability: Water Absorb Possible moves:

Rival Characters

Hugh

Will get back his sisters Purrloin.
Trapinch → Vibrava → Flygon♂	Will evolve off-screen (or maybe, panel). Ability: Levitate Possible new moves: Bug Buzz Bulldoze Draco Meteor Sand Tomb Dragon Breath Rock Slide
Pidove → Tranquill → Unfezant♀	Ability: Super Luck Possible new moves:
Tynamo → Eelektrik → Eelektross♂	I'm hoping it evolves on panel. Ability: Levitate Possible new moves:
Bouffalant♂	Ability: Reckless Possible moves:

Leo


Deino → Zweilous♂	Ability: Hustle Possible new moves:

Supporting Characters

Looker

Will be the travelling companion to Lack-Two.
Croagunk♂	Maybe this is where Croagunk will die (just like the games). Ability: Dry Skin Possible new moves:

N

Will work with Blake and Whitley to stop Ghetsis, however he planed for N to come and traps Zekrom.
Zekrom	Ability: Teravolt Possible new moves:

Bianca


Oshawott♂	Ability: Torrent Possible new moves:
Litwick → Lampent♀	Has become Bianca's main battling Pokémon. Ability: Flash Fire Possible new moves:

Cheren


Snivy♂	Cheren now trusts his Snivy for battles again. Ability: Overgrow Possible new moves:
Pidove → Tranquill → Unfezant♂	Ability: Big Pecks Possible new moves:
Boldore → Gigalith♂	Ability: Sturdy Possible new moves:
Patrat♀	Ability: Keen Eye Possible moves:
Herdier♂	Ability: Intimidate Possible moves:

Iris

Has been granted the position of champion by the Elite Four after Alder disappeared.
Axew → Fraxure → Haxorus♂	Ability: Mold Breaker Possible new moves: Dragon Pulse Dragon Claw Guillotine Outrage Swords Dance
Druddigon♀	Ability: Rough Skin Possible new moves:
Lapras♀	Ability: Shell Armor Possible new moves:
Hydreigon♂	Ability: Levitate Possible moves:

Alder

Has been hiding in his house at Floccesy Town after losing to N.
Bouffalant♂	Ability: Sap Sipper Possible new moves:
Accelgor♂	Ability: Sticky Hold Possible new moves:
Escavalier♂	Ability: Shell Armor Possible new moves:
Vanilluxe♀	Ability: Ice Body Possible new moves:

Yuki


Wingull♀	Ability: Keen Eye Possible new moves:

Yuko


Sunkern → Sunflora♂	Ability: Solar Power Possible new moves:

Maya


Combee♂	Ability: Honey Gather Possible new moves:

Benga

Has been searching for Alder for two years.
Gible → Gabite → Garchomp♂	Ability: Sand Veil Possible new moves:
Larvesta → Volcarona♂	Ability: Flame Body Possible new moves:
Dratini → Dragonair → Dragonite♂	Ability: Inner Focus Possible moves:

Rood

Has stared Ex-Team Plasma to bring Pokémon they stole back to there owners.
Lampent♂	Ability: Flame Body Possible new moves:

Temporary

Zorua♀

Was the one N released, and will be given to Whi-Two.

Ability: Illusion
Possible new moves:

Magician


Corphish♀	Ability: Shell Armor Possible new moves:

White


Amanda♀	Ability: Overgrow Possible new moves:
Darlene♀	Ability: Chlorophyll Possible new moves:
Dorothy♀	Ability: Limber Possible new moves:
Nancy♀	Ability: Healer Possible new moves:
Solly♂	Ability: Magic Guard Possible new moves:
Barbara♀	Ability: Big Pecks Possible new moves:

In the BW Agency

Gigi♀

Ability: Blaze

Possible new moves:

Black

Will be taken out of the Light Stone.
Brav♂	Ability: Sheer Force Possible new moves:
Musha♂	Ability: Forewarn Possible new moves:
Bo♂	Ability: Blaze Possible new moves:
Tula♂	Ability: Unnerve Possible new moves:
Costa♂	Ability: Solid Rock Possible new moves:

Temporary

Reshiram

Will leave Black once its awaken from the Light Stone.

Ability: Turboblaze
Possible new moves:

Evil Characters

Colress

Is making people think he's the new leader of Team Plasma, when he isn't.
Beheeyem♂	Ability: Telepathy Possible new moves: Psychic Zen Headbutt Gravity
Klink	Ability: Minus Possible new moves:
Klinklang	Ability: Plus Possible new moves:
Tornadus♂	Ability: Prankster (in Incarnate Forme) Regenerator (in Therian Forme) Possible new moves:
Thundurus♂	Ability: Prankster (in Incarnate Forme) Volt Absorb (in Therian Forme) Possible new moves:
Landorus♂	Ability: Sand Force (in Incarnate Forme) Intimidate (in Therian Forme) Possible new moves:
Kyurem	Has been taken from Zinzolin. Ability: Pressure Possible new moves:
Magnezone	Ability: Magnet Pull Possible moves:
Rotom	Ability: Levitate Possible moves:

Ghetsis

Is still the true mastermind behind Team Plasma.
Hydreigon♂	Ability: Levitate Possible new moves:
Eelektross♂	Ability: Levitate Possible new moves:
Seismitoad♂	Ability: Swift Swim Possible new moves:
Cofagrigus♂	Ability: Mummy Possible new moves:
Volcarona♂	Ability: Flame Body Possible new moves:
Drapion♂	Ability: Battle Armor Possible moves:

Zinzolin


Cryogonal	Ability: Levitate Possible new moves:
Vanilluxe♀	Was one of the Pokémon Zinzolin prepared for the Unova League. Ability: Snow Warning Possible moves:
Beartic♂	Was one of the Pokémon Zinzolin prepared for the Unova League. Ability: Snow Cloak Possible moves:
Weavile♂	Ability: Pressure Possible moves:

Sun & Moon chapter

Main Characters

Sun


Dollar♂	Ability: Technician Possible new moves: Fury Swipes Thief Feint Assurance Beat Up Z-Move: Black Hole Eclipse
En♂	Ability: Blaze Possible new moves: Lick Fire Fang Bite Flamethrower Fury Swipes Darkest Lariat Z-Move: Malicious Moonsault
Baht♀	Ability: Schooling Possible new moves: Z-Move: Hydro Vortex
Sandygast → Palossand♂	Ability: Water Compaction Possible moves:
Zygarde	Will join Sun. Ability: Power Construct Possible new moves: Bulldoze Dragon Breath Outrage Extreme Speed Frustration Haze Core Enforcer

Travel with

Rotom

Will go inside the Rotom Pokédex.*

Ability: Levitate
Possible new moves:

Moon


Grubbin♀	Ability: Swarm Possible new moves:
Mareanie → Toxapex♂	Ability: Merciless Possible new moves:
Grimer → Muk♂	Ability: Poison Touch Possible new moves:
Rowlet → Dartrix → Decidueye♂	Ability: Overgrow Possible new moves: Z-Move: Sinister Arrow Raid

Supporting Characters

Hau


Pichu → Pikachu → Raichu♂	Ability: Surge Surfer Static (as Pichu and Pikachu) Possible new moves:
Komala♂	Ability: Comatose Possible new moves:
Popplio → Brionne → Primarina♀	Ability: Torrent Possible moves:

Lillie


Nebby	Ability: Shadow Shield Sturdy (as Cosmoem) Unaware (as Cosmog) Possible new moves:

Gladion


Type: Null	Ability: Battle Armor Possible new moves:
Porygon	Ability: Download Possible new moves:

Professor Kukui


Rockruff → Lycanroc♀	Ability: Keen Eye Possible new moves:
Munchlax♂	Ability: Thick Fat Possible new moves:
Stufful	Ability: Fluffy Possible moves:

Anabel

Considering her role in Sun & Moon, shes going to appear later.
Raikou	Ability: Pressure Possible new moves:

Past Characters

Main Characters

Red

I'm thinking he'll come back in the Sun & Moon chapter.
Poli♂	Ability: Damp Possible new moves: Z-Move: Hydro Vortex
Saur♂	Ability: Overgrow Thick Fat (as Mega Venusaur) Possible new moves: Z-Move: Bloom Doom
Pika♂	Ability: Static Possible new moves: Z-Move: Catastropika
Snor♂	Ability: Immunity Possible new moves: Z-Move: Pulverizing Pancake
Vee♂	Ability: Synchronize Adaptability (as Eevee) Possible new moves: Z-Move: Shattered Psyche
Gyara♂	Will use Lysandre's Gyaradosite to Mega Evolve. Ability: Intimidate Mold Breaker (as Mega Gyarados) Possible new moves: Z-Move: Hydro Vortex
Aero♂	Ability: Rock Head Tough Claws (as Mega Aerodactyl) Possible new moves: Z-Move: Continental Crush

In Bill's PC

Nidorino♂	Ability: Poison Point Possible new moves:
Diglett♂	Ability: Arena Trap Possible new moves:
Sandshrew♂	Ability: Sand Veil Possible new moves:
Bellsprout (multiple)♂♀	Fearow♂	Caterpie → Metapod → Butterfree♂
Nidoqueen♀	Nidoking (multiple)♂	Victreebel (multiple)♂♀
Weepinbell (multiple)♂♀	Exeggcute (multiple)♂♀	Parasect (multiple)♂♀

Blue

I'm thinking he'll come back in the Sun & Moon chapter.
Scyther → Scizor ↔ Mega Scizor♂	Ability: Swarm Technician (as Mega Scizor) Possible new moves: X-Scissor Bullet Punch Night Slash Vacuum Wave Bug Bite Swords Dance
Charmander → Charmeleon → Charizard ↔ Mega Charizard Y♂	Ability: Blaze Drought (as Mega Charizard Y) Possible new moves: Dragon Claw Flare Blitz Metal Claw Power-Up Punch
Golduck♂	Ability: Cloud Nine Possible new moves: Zen Headbutt Aqua Tail Wonder Room
Machoke → Machamp♂	Ability: Guts Possible new moves: Low Sweep Dual Chop Sky Uppercut High Jump Kick Final Gambit
Porygon → Porygon2 → Porygon-Z	Has evolved off-screen. Ability: Adaptability Possible new moves: Lock-On Recover Secret Power Signal Beam
Rhydon → Rhyperior♂	Ability: Lightning Rod Possible new moves: Drill Run Stone Edge Smack Down Earth Power

At Viridian Gym

Pidgeot♂	Ability: Keen Eye Possible new moves:
Ninetales♂	Ability: Flash Fire Possible new moves:
Exeggutor♂	Ability: Chlorophyll Possible new moves:
Alakazam♂	Ability: Synchronize Possible new moves:
Arcanine♂	Ability: Flash Fire Possible new moves:
Pumpkaboo♂	Ability: Frisk Possible new moves:

Green

I'm thinking she'll come back in the Sun & Moon chapter.
Jiggly♀	Ability: Cute Charm Possible new moves: Echoed Voice Play Rough Hyper Voice Dazzling Gleam
Snubbull → Granbull♂	Ability: Quick Feet Run Away (as Snubbull) Possible new moves:
Blasty♂	Ability: Torrent Mega Launcher (as Mega Blastoise) Possible new moves:
Ditty	Ability: Limber Possible new moves:
Clefy♂	Ability: Cute Charm Possible new moves:
Nido♀	Ability: Poison Point Possible new moves:
Ririri♀	Ability: Cute Charm Possible new moves:

In Bill's PC

Weedle♂	Ability: Shield Dust
Abra♀	Ability: Synchronize Possible new moves:
Articuno	Ability: Pressure Possible new moves:
Zapdos	Ability: Pressure Possible new moves:
Moltres	Ability: Pressure Possible new moves:

Yellow

I'm thinking she'll come back in the Sun & Moon chapter.
Ratty♂	Ability: Guts Possible new moves:
Dody♂	Ability: Early Bird Possible new moves:
Gravvy♂	Ability: Sturdy Possible new moves:
Omny♂	Ability: Swift Swim Possible new moves:
Kitty♂	Ability: Compound Eyes Possible new moves:
Chuchu♀	Ability: Static Possible new moves:

Gold


Aibo♂	Ability: Technician Run Away (as Aipom) Possible new moves:
Polibo♂	Ability: Water Absorb Possible new moves:
Exbo♂	Ability: Blaze Possible new moves:
Sunbo♀	Ability: Chlorophyll Possible new moves:
Sudobo♂	Ability: Sturdy Possible new moves:
Togebo♂	Ability: Hustle Possible new moves:
Pibu♂	Ability: Static Possible new moves:
Spiky-eared Pichu♀	I think shes now traveling with Gold.* Ability: Static Possible new moves:

In Bill's PC

Tibo♂	Ability: Swift Swim Possible new moves:
Remoraid (x20)♂	Ability: Sniper Possible new moves:

At Home

Lickitung♂	Sandshrew♀	Oddish♀
Drowzee♂	Krabby♂	Chansey♀
Weedle♀	Exeggcute♂	Kakuna♂
Murkrow♀

Silver


Sneasel → Weavile♂	Ability: Pressure Inner Focus (as Sneasel) Possible new moves:
Horsea → Seadra → Kingdra♀	Ability: Swift Swim Poison Point (as Seadra) Possible new moves:
Totodile → Croconaw → Feraligatr♂	Ability: Torrent Possible new moves:
Ursaring♂	Has been given back. Ability: Guts Possible new moves:
Murkrow → Honchkrow♂	Ability: Insomnia Possible new moves:
Gyarados♂	Ability: Intimidate Possible new moves:

Crystal


Chumee♀	Ability: Oblivious Possible new moves:
Archy♂	Ability: Intimidate Possible new moves:
Parasee♀	Ability: Dry Skin Possible new moves:
Bonee♂	Ability: Lightning Rod Possible new moves:
Natee♀	Ability: Early Bird Possible new moves:
Megaree♀	Ability: Overgrow Possible new moves:

In Bill's PC

I don't want to put ALL of Crystal's Pokémon here.
Monlee♂	Ability: Iron Fist Possible new moves:
Mymee♀	Ability: Filter Possible new moves:

Ruby


Nana♀	Ability: Intimidate Possible new moves:
Kiki♀	Ability: Cute Charm Possible new moves:
Rara♀	Ability: Synchronize Pixilate (as Mega Gardevoir) Possible new moves:
Mumu♂	Ability: Torrent Swift Swim (as Mega Swampert) Possible new moves:
Feefee♀	Ability: Marvel Scale Swift Swim (as Feebas) Possible new moves:
Fofo♀	Ability: Forecast Possible new moves:

Sapphire


Rono♂	Ability: Sturdy Filter (as Mega Aggron) Possible new moves:
Chic♀	Ability: Blaze Speed Boost (as Mega Blaziken) Possible new moves:
Troppy♂	Ability: Chlorophyll Possible new moves:
Phado♂	Ability: Sturdy Possible new moves:
Relly♂	Has returned from the sea. Ability: Rock Head Possible new moves:
Kirly♂	Ability: Steadfast Inner Focus (as Mega Gallade) Trace (as Kirlia) Possible new moves:

At Sea

Lorry♂

Ability: Oblivious

Possible new moves:

Emerald


Treecko → Grovyle → Sceptile ↔ Mega Sceptile♂	Ability: Overgrow Lightning Rod (as Mega Sceptile) Possible new moves:
Sudowoodo♀	Ability: Rock Head Possible new moves:
Dusclops♂	Ability: Pressure Possible new moves:
Snorlax♀	Ability: Thick Fat Possible new moves:
Mr. Mime♂	Ability: Soundproof Possible new moves:
Mantine♀	Ability: Swift Swim Possible new moves:

Diamond


Lax♂	I hope Lax meets his parents. Ability: Pickup Possible new moves:
Tru♂	Ability: Overgrow Possible new moves:
Don♂	Ability: Sturdy Possible new moves:
Kit♂	Ability: Own Tempo Possible new moves:
Moo♂	Ability: Thick Fat Possible new moves:
Reg	Ability: Slow Start Possible new moves:
Rotom	Ability: Levitate Possible new moves:

Pearl


Chatler♂	Ability: Tangled Feet Possible new moves:
Chimler♂	Ability: Blaze Possible new moves:
Rayler♂	Ability: Intimidate Possible new moves:
Zeller♂	Is starting to like Pearl more. Ability: Swift Swim Possible new moves:
Tauler♂	Ability: Anger Point Possible new moves:
Digler♂	Ability: Sand Veil Possible new moves:

Platinum


Ponyta → Rapidash♂	Ability: Flash Fire Possible new moves:
Piplup → Prinplup → Empoleon♀	Ability: Torrent Possible new moves:
Lopunny ↔ Mega Lopunny♀	Ability: Cute Charm Scrappy (as Mega Lopunny) Possible new moves:
Froslass♀	Ability: Snow Cloak Possible new moves:
Cherrim♀	Ability: Flower Gift Possible new moves:
Pachirisu♀	Ability: Run Away Possible new moves:

X

I'm thinking he'll come back in the Sun & Moon chapter.
Kanga and Li'l Kanga♀	Ability: Scrappy Parental Bond (as Mega Kangaskhan) Possible new moves: Sucker Punch Retaliate Dizzy Punch Chip Away Brick Break Blizzard
Marisso♂	Ability: Overgrow Possible new moves: Needle Arm Hammer Arm Belly Drum Energy Ball Seed Bomb Focus Blast
Salamè♂	Ability: Blaze Tough Claws (as Mega Charizard X) Possible new moves: Flamethrower Dragon Claw Inferno Heat Wave Sunny Day Solar Beam
Élec♂	Ability: Lightning Rod Intimidate (as Mega Manectric) Possible new moves: Thunder Fang Thunderbolt Fire Fang Signal Beam Howl
Garma♂	Ability: Levitate Shadow Tag (as Mega Gengar) Possible new moves: Shadow Ball Hypnosis Sludge Wave Astonish Night Shade
Rute♂	Ability: Hyper Cutter Aerilate (as Mega Pinsir) Possible new moves: X-Scissor Guillotine Submission Seismic Toss Dig Vice Grip Close Combat

Yvonne Gābena

I'm thinking she'll come back in the Sun & Moon chapter.
Fletchy♀	I'm not sure how or when it will evolve. Ability: Flame Body Big Pecks (as Fletchling) Possible new moves: Heat Wave Roost Brave Bird Return Tailwind
Veevee♀	Ability: Cute Charm Run Away (as Eevee) Possible new moves: Moonblast Charm Fairy Wind Dazzling Gleam
Croaky♂	Ability: Battle Bond Possible new moves: Shadow Sneak Night Slash Role Play Water Pulse Substitute
Rhyrhy♂	Ability: Rock Head Possible new moves: Horn Attack Horn Drill Drill Run Megahorn Chip Away Stone Edge
Solsol♀	Ability: Super Luck Magic Bounce (as Mega Absol) Possible new moves: Future Sight Perish Song Foul Play Punishment Sucker Punch Play Rough

Supporting Characters

Pryce


Seel (×2)♀	Ability: Thick Fat Possible new moves:
Swinub♀	Ability: Oblivious Possible new moves:
Delibird♂	Is the same one the Masked Man used. Ability: Vital Spirit Possible new moves:
Gastly♂	Ability: Levitate Possible new moves:
Houndour♂	Ability: Flash Fire Possible new moves:
Ariados♂	Ability: Swarm Possible new moves:

In the Past

La Prus♂

La Pris♀

La Glace♂

Wally


Kecleon♂	Ability: Color Change Possible new moves:
Cacnea → Cacturne♂	Ability: Sand Veil Possible new moves:
Roselia → Roserade♂	Ability: Natural Cure Possible new moves:
Flygon♂	Ability: Levitate Possible new moves:
Altaria♂	Ability: Natural Cure Possible new moves:
Magnezone	Ability: Sturdy Possible new moves:

Trevor


Flabébé → Floette → Florges♀	Ability: Flower Veil Possible new moves: Petal Blizzard Aromatherapy Flower Shield Magical Leaf
Fennekin → Braixen → Delphox♀	Ability: Blaze Possible new moves: Flamethrower Switcheroo Blast Burn Future Sight

Shauna


Neco-P♀	Ability: Normalize Possible new moves: Double Slap Sing Fury Swipes Tail Whip
Tri-P♂	Ability: Fur Coat Possible new moves: Tackle Headbutt Baby-Doll Eyes Hyper Voice Secret Power

Tierno


Corphish → Crawdaunt♂	Ability: Shell Armor Possible new moves: Bubble Beam Crabhammer Vice Grip Crunch Knock Off Aqua Jet

Gurkinn


Heracross ↔ Mega Heracross♂	Ability: Guts Skill Link (as Mega Heracross) Possible new moves: Megahorn Brick Break Fury Attack Horn Attack

Korrina


Riolu → Lucario ↔ Mega Lucario♂	Has been Korrina's starter Pokémon given by Gurkinn. Ability: Steadfast Adaptability (as Mega Lucario) Possible new moves: Close Combat Extreme Speed Metal Claw Giga Impact

Diantha


Ralts → Kirlia → Gardevoir ↔ Mega Gardevoir♀	Ability: Trace Pixilate (as Mega Gardevoir) Possible new moves: Moonblast Hypnosis Dream Eater Future Sight Play Rough Dazzling Gleam

Emma/Essentia


Mimi♀	Ability: Keen Eye Possible new moves:

AZ


Floette♀	Ability: Flower Veil Possible new moves:
Golurk	Ability: Iron Fist Possible new moves:

Evil Characters

Giovanni


Weedle → Kakuna → Beedrill ↔ Mega Beedrill♂	Ability: Swarm Adaptability (as Mega Beedrill) Possible new moves:
Cloyster♂	Ability: Shell Armor Possible new moves:
Nidoqueen♀	Ability: Rivalry Possible new moves:
Golem♂	Ability: Rock Head Possible new moves:
Nidoking♂	Ability: Rivalry Possible new moves:
Dugtrio♂	Ability: Sand Veil Possible new moves:
Rhyhorn♂	Ability: Lightning Rod Possible new moves:
Rhydon♂	Ability: Rock Head Possible new moves:
Crobat♀	Ability: Inner Focus Possible new moves:
Aggron♂	Ability: Rock Head Possible new moves:

Lance


Dratini → Dragonair → Dragonite♂	Ability: Inner Focus Possible new moves:
Magikarp → Gyarados♂	Ability: Intimidate Swift Swim (as Magikarp) Possible new moves:
Horsea → Seadra → Kingdra♂	Ability: Sniper
Dragonair (multiple)♂♀	Ability: Shed Skin Possible new moves:
Aerodactyl (multiple)♂♀	Ability: both Rock Head and Pressure Possible new moves:
Dragonite♀	Ability: Inner Focus Possible new moves:
Pupitar → Tyranitar♂	Ability: Sand Stream Possible new moves:

Archie


Walrein (multiple)♂♀	Ability: Thick Fat Possible new moves:
Tentacruel♂	Is the same one Guile Hideout used and the one from Team Aqua HQ. Ability: Liquid Ooze Possible new moves:
Surskit → Masquerain♂	Ability: Intimidate Swift Swim (as Surskit) Possible new moves:
Starmie (×4)	Ability: both Illuminate and Natural Cure Possible new moves:

At Team Aqua HQ

Archie no longer has access to these Pokémon.
Qwilfish♂	Mantine♀	Goldeen♀
Magikarp♂	Remoraid♀	Chinchou♂
Shellder♂	Sharpedo♂	Huntail♂
Corsola♀	Barboach♀	Wailmer♂
Horsea♂

Amber


Pelipper♂	Ability: Keen Eye Possible new moves:
Nincada → Ninjask♀	Ability: Speed Boost Compound Eyes (as Nincada) Possible new moves:
Nincada → Shedinja	Ability: Wonder Guard Compound Eyes (as Nincada) Possible new moves:
Gorebyss♀	Ability: Swift Swim Possible new moves:
Sharpedo ↔ Mega Sharpedo♂	Ability: Rough Skin Strong Jaw (as Mega Sharpedo) Possible new moves:

Left at the Seafloor Cavern

We won't be seeing these 4 anytime soon.
Carvanha♂	Ability: Rough Skin
Volbeat (×3)♂	Ability: both Illuminate and Swarm

Maxie


Swellow♂	Ability: Guts Possible new moves:
Houndoom (multiple)♂♀	Ability: both Early Bird and Flash Fire Possible new moves:

Blaise


Slugma (×2)♂♀	Ability: Flame Body Possible new moves:
Swellow♀	Ability: Guts Possible new moves:
Armaldo♂	Ability: Battle Armor Possible new moves:
Camerupt ↔ Mega Camerupt♂	Ability: Magma Armor Sheer Force (as Mega Camerupt) Possible new moves:

Xerosic

All of Essentia's Pokémon have been Xerosic's the whole time.
Inkay → Malamar♂	Ability: Contrary Possible new moves:
Crobat (x4)♂	Ability: Inner Focus Possible new moves:
Trevenant♂	Ability: Frisk Possible new moves:
Phantump♂	Ability: Natural Cure Possible new moves:
Hawlucha (x4)♂	Ability: Limber Possible new moves:

Malva


Pyroar♀	Ability: Rivalry Possible new moves:
Talonflame♂	Ability: Flame Body Possible new moves:

Lysandre


Gyarados ↔ Mega Gyarados♂	Ability: Intimidate Mold Breaker (as Mega Gyarados) Possible new moves: Hyper Beam Aqua Tail Scald Water Pulse Thrash Twister
Pyroar♂	Ability: Unnerve Possible new moves: Overheat Crunch Incinerate Heat Wave Take Down
Mienfoo♂	Ability: Inner Focus Possible new moves: Reversal Vital Throw Force Palm Double Team Bounce

Legendary Pokémon

Mortality duo

Xerxer	Ability: Fairy Aura Possible new moves: Moonblast Calm Mind Aromatherapy Nature Power Megahorn Misty Terrain
Yveltal	Ability: Dark Aura Possible new moves: Hurricane Dark Pulse Foul Play Dragon Rush Hyper Beam Focus Blast Disable