1. Attack on Titan

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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 8 before they get that desperate for ideas. 

 

2. Free!

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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.

 

3. Kill La Kill

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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.