Staraptor: Ryuko Matoi, the hot-blooded protagonist out to avenge her father's murder. Besides their similar coloration and distinctive red streak, Staraptor and Ryuko are both looked down upon by elitists.
Cobalion: Satsuki Kiryuin rules the Honnoji Academy with her unflappable resolve, high class sophistication, and nigh-invincible eyebrow game. It only fits that she be represented by this cooly refined member of the legendary "Swords of Justice".
Scizor: The key to everything lies in the secrets of the red Scissor Blade.
Mega-Aggron: Ira Gamagori is the sworn shield of Satsuki, has a thing for being covered in spikes, and is built for taking a LOT of punishment.
Scrafty: This pokemon has an existentially serious issue with holding onto its clothing, much like everybody in this series.
Ludiculo: The plot.
Clefable: One of the first pokemon ever created, Clefable literally transforms using the power of the moon... stone.
Sylveon: This fairy-type is capable of producing endless amounts of pretty ribbons and bows that appear out of nowhere, just like in Sailor Moon's transformation sequences.
Mega-Gardevoir: Achieves highest power level by putting on a white dress.
Roserade: You know who else uses roses as a weapon and covers their face? Tuxedo Mask.
Meowth: Essential to the Sailor Moon lore is her guardian cat named Luna, who can speak perfect english and has a gold icon in the middle of her head. Meowth, that's right indeed.
Solrock: Shit, why is that there? I meant to put in Lunatone! How do I undo this? Oh fuck... fuck fuck fuck fuck SHIT.
Vaporeon- Milotec- Dragonair- Swanna: 4 Breathtakingly Beautiful Aquatic Creatures.
Machoke: Totally rocks a Speedo. Perfectly hairless body.
Lickitung: Most of the audience of this show.
Cubone: Eren Jaeger, a young man traumatized by the death of his mother, but determined to continue fighting for humanity's freedom. He seems most comfortable surrounded by oversized bones.
Greninja (shiny): Mikasa Ackerman, the badass with a red scarf and elite ninja skills. The Internet's favorite character.
Smoochum: Armin Arlert, the tiny weak thing with a mop of blonde hair (NAILED IT).
Regigigas: Gigantic, unknowable... and hilariously slow, just like the Colossal Titan.
Bastiodon: If there are two things that best represent this series it's "large walls" and "unsettling grinning faces".
Doublade: The preferred weapon of the Scouting Legion are twin swords. I tried to find a pokemon that looked like a giant boxcutter, but we'll probably have to wait until gen 9 before they get that desperate for ideas.
Mega-Ampharos: FLOWING LOCKS OF ELECTRICALLY CHARGED HAIRRRRRR!
Mega-Mewtwo Y: FRIEZA'S FINAL FORMMMMMM!
Mega-Lucario: SOMETHING TWELVE-YEAR-OLDS THINK IS COOLLLLLLL!
Mega-Manetric: EVEN MORE SPIKY BLONDE HAIRRRRR!!!!
Mega-Rayquaza: A CHARACTER THAT'S SO POWERFUL IT MAKES THE WHOLE ENTERPRISE SEEM LAUGHABLY RIDICULOUSSSSS!
Yamask: Almost all the events in this series can be traced back to the uncovering of a mysterious Stone Mask.
Blaziken: A giant fire-breathing chicken? MAGICIAN'S RED!
Escavalier: Pointy armored knight? SILVER CHARIOT!
Jynx: An unfortunate caricature of a woman and/or minority.
Hitmonchan: ORA ORA ORA ORA ORA ORA!!!!!!!
Hitmonlee: MUDA MUDA MUDA MUDA MUDA!!!!!!!!!
Snorlax: Big, fuzzy, and looks incredibly comfortable to sleep on? It can be Snorlax or Totoro.
Emboar: A badass pig with a smoking problem aka Porco Rosso.
Golurk: An ancient piece of technology you feel kind of sad for? I'm pretty sure it's Golurk, or the robots from Castle in the Sky
Venipede: Not since Nausicaa have I been so intimidated by giant bugs like this.
Xerneas: Ok come on, that's literally the giant nature god from the end of Princess Mononoke. We're onto you, Nintendo.
Phantump: This one is a little less specific, but you have to acknowledge the thematic overlap with innocent-yet-spooky nature spirits and (if you believe the pokedex from Pokemon X/Y) children that die tragically.