Mega Ninetales
Type: Fire/Ghost
Possible abilities: Shadow Tag, Cursed Body, Magic Bounce, Flash Fire
Possible moveset additions: Shadow Ball
Reasoning: Now there's a couple of types I could see fitting it, Psychic, Dark, Fairy. But Ninetales and its inspiration, kitsunes, are depicted as having supernatural abilities and can inflict curses, so with that in mind I think Ghost fits the best. Additionally, Kanto is sorely lacking in Ghost types (with only the Gengar line comprising Kanto's selection of Ghosts) and adding some Ghost type Megas would help fill that balance. Also add Shadow
Mega Persian
Type: Normal/Dark
Possible abilities: Infiltrator, Super Luck
Reasoning: I never really considered it until recently, but Normal/Dark fits Persian so well seeing as the Persian line are sneaky cats that steal coins, and in retrospect I have to wonder why Meowth and Persian weren't given Dark way back in 2nd gen when the type was created. Anyway, Kanto is also lacking Dark types and didn't get any until Mega Gyarados (and if Eeveelutions are added in, Umbreon), so this helps with another critical balancing issue in Kanto's lineup (Kanto is really lacking in several types).
Mega Golduck
Type: Water/Psychic
Possible abilities: Hydration, Water Absorb
Reasoning: Can someone tell me why a Pokemon who's already explicitly been connected to the Psychic type (to the point where the English name of its pre-evolved form is literally a combination of the words "psychic" and "duck") is not Water/Psychic? Something that's bugged me for a while.
Mega Rapidash
Type: Fire/Flying
Ability: Aerilate
Reasoning: I really think the alicorn route is a good direction for Rapidash's Mega. I chose Aerilate as its ability because it's a quick and easy way to give him some Flying type moves since he already has several great Normal type moves to draw from
Mega Marowak
Type: Ground/Ghost
Possible abilities: Shadow Tag, Cursed Body
Possible moveset additions: Shadow Sneak, Shadow Punch, Phantom Force
Reasoning: Cubone and Marowak's theme is that they wear the skull of their dead mother, so this idea furthers that concept by having its dead mother possess it. Again, this is another Mega idea that would help fix type balance issues in Kanto.
Mega Noctowl
Type: Psychic/Flying
Possible abilities: Magic Guard, Magic Bounce, Synchronize, Tinted Lens
Reasoning: Its dex entry claims it's capable of complex thought, and its nocturnal abilities could be justified as a sort of psychic ability.
Mega Ledian
Type: Bug/Fighting
Possible abilities: Iron Fist, Technician
Possible moveset additions: Flying Press, Close Combat
Reasoning: Take a look at Ledian's hands. Look a lot like boxing gloves don't they? Also Ledian has several punching moves in its moveset.
Mega Sunflora
Type: Grass/Fire
Ability: Drought
Possible moveset additions: Fire Spin, Flame Wheel, Flamethrower, Heat Wave
Reasoning: Sunflora is a sunflower Pokemon. Emphasis on "sun". Do I need to say anymore?
Mega Girafarig
Type: Psychic/Dark
Possible abilities: Strong Jaw, Intimidate
Possible moveset additions: Bite, Feint Attack
Reasoning: Girafarig's tail is pretty menacing. It doesn't sleep, it lashes out and bites people. Sounds like a Dark type to me.
Mega Lugia
Possible types: Flying/Water or Psychic/Water
Reasoning: Lugia has a very strong connection to the sea in its lore, it's typically found in deep sea areas and its dex entry. Ideally I'd replace Psychic because Lugia's connection to Psychic never made much sense (as it's never been shown to have psychic abilities in its lore), but alternatively they could remove its ability to fly and replace Flying.
Mega Milotic
Type: Water/Fairy
Possible abilities: Multiscale, Serene Grace, Healer
Possible moveset additions: Dazzling Gleam, Draining Kiss
Reasoning: Milotic's beauty lends itself well to a mermaid theme, which they could utilize for its Mega. Mermaids are technically considered a type of fairy, and Milotic already has the ability to calm hostile emotions so the typing feels natural.
Mega Huntail
Type: Water/Dark
Ability: Strong Jaw
Reasoning: It has a lot of Dark type moves to the point where I thought it was already this to begin with. Also, its dex entry states that it lives in undersea trenches.
Mega Gorebyss
Type: Water/Psychic
Possible abilities: Synchronize, Inner Focus
Reasoning: Similar reasoning to Huntail.
Mega Luxray
Type: Electric/Dark
Ability: Strong Jaw
Reasoning: Has night vision abilities and learns several Dark type moves.
Mega Mismagius
Type: Ghost/Fairy
Ability: Magic Guard
Possible moveset additions: Disarming Voice, Fairy Wind
Reasoning: Is based on a banshee, which is a type of fairy, and can chant incantations that can bring happiness or torment.
Mega Electivire
Type: Electric/Fighting
Ability: Motor Drive
Possible moveset additions: Close Combat, Mach Punch, Superpower
Reasoning: Very physical and can learn several Fighting type moves. Plus we need more interesting Electric type combos.
Mega Magmortar
Type: Fire/Poison
Possible abilities: Flash Fire, White Smoke
Possible moveset additions: Poison Jab
Reasoning: Given a second type to parallel Mega Electivire. Magmortar learns several Poison type moves and Poison fits its theme.
Mega Uxie/Mesprit/Azelf
Type: Psychic/Fairy
Ability: Levitate
Possible moveset additions: Disarming Voice, Moonblast
Reasoning: Blatantly based on pixies.
Mega Serperior
Type: Grass/Dragon
Ability: Contrary
Possible moveset additions: Dragonbreath
Reasoning: Elegant serpent, dragon fits the species.
Mega Samurott
Type: Water/Steel
Possible abilities: Hyper Cutter, Shell Armor
Possible moveset additions: Iron Head
Reasoning: Samurai theme lends itself well to either Fighting or Steel. I chose Steel because Emboar is already Fighting and it would feel repetitive if two of the Unova starters were part Fighting.
Mega Beartic
Type: Ice/Water
Ability: Swift Swim
Reasoning: Already has a strong connection to Water, it has a Water themed ability, several Water type moves, and the polar bears it's based on can swim.
Mega Braviary
Type: Fighting/Flying
Possible abilities: Anger Point, Moxie
Possible moveset additions: Close Combat, Flying Press
Reasoning: Explicitly referred to as a warrior bird in dex entries.
Mega Florges
Type: Fairy/Grass
Ability: Leaf Guard
Reasoning: Part of its body is already a flower and it has a strong connection to plants.
Mega Xerneas
Type: Fairy/Grass
Ability: Fairy Aura
Reasoning: Lives in forested habitats and plants are commonly associated with life. Also learns several Grass type moves.