Pokemon Cinder/Rust/Rot

http://titleknown.tumblr.com/post/140043903673/pokemon-cinderrustrot-proposal-part-1

You start out as a poor, dark-skinned kid (Who, when asked “Are you a boy, or a girl?” can answer Boy Girl or Nah/Neither)  in a crummy; huge apartment complex known as Absol Apartments, with your mother making ends meet by renting out a room to a strange person-of-indistinct-gender known as Professor Willow. You rifle through his stuff and find three Pokeballs, before you hear them getting attacked by a wild Pikachu (Which infests the Apartments and is considered a pest-species in Kolomb) and having to take one to rescue them.
The three-starter's types are a Neon Sign-like Electric-type cat which also gains elements of a Motorcycle and a jousting knight as well as the Fighting type as it evolves, a pure Flying type that's just a ball of ethereal wings that gets more angelic looking as it evolves (While still remaining mono-Flying), and a Ground type that looks like a snake made of glitter and gets the Fairy type as it evolves to gain a more fairy dust/comet dust theme.
These three Poke's, forming a rough “trinity” ala Fire/Water/Grass or Fighting/Dark/Psychic are glitzy to contrast with the setting and illuminate the themes of hope within darkness, as happens when Professor Willow decides to give you the Pokemon after you save them to hopefully fix things in this continent.
Tho, another Poke of your opposing  type gets taken by a mysterious trainer
And there's also the fact that Professor Willow may or may not be actually dead, as a sidequest would lead you to find what may be their body and, when asked about it, they'll say “People believe what they want to believe” and walk through a wall. When you see them again the next day, they'll respond when asked “I don't recall there ever being a wall there,” and give you a TM for Destiny Bond.
The first area is the absolutely huge, Pokemon-infested Absol Apartments, which you need to leave to get to the larger world.
Mold (Grass/Ghost), Rustpipe (Steel/Water),  Ashspider (Bug/Fire)The Pokemon that show up around here include a Fire/Bug soot-sprite-thing that evolves into a flaming; pyromaniacal wood-fire-ash-Harvestman, a Water/Steel pipe-snake-mon who evolves into a weird water-spewing pipe-maze snakeball-hydra-thingy, and an unsettling black-mold-patch-with-a-warped-face Grass-type thing that grows more grotesque and contorted as it evolves into a Grass/Ghost type. Yes they are themed after grubby equivalents to the three typical “starter” types. And, of course, there are also the ever-present Pikachu infestations.
But wait, you say, without wild grass? Yes! I forgot to mention this in my previous bit, but in towns, there are Pokemon encounters without wild grass in this game, and this introduces you to it, making the wild ironically safer than the towns.
And then, by the end, you meet a strange trainer, with a halting; unsettling manner of speech whose face is one you cannot quite make out, who talks about how much he doesn't like people and then attacks. He uses the main Pokemon you didn't pick, and th
But, when you arrive to leave the apartment/city limits; you've found the police have blocked off everywhere and are looking to beat the crap out of you. But, just as they close in, a member of the “evil team” they hope to destroy, comes to rescue you, and holds them off as they give you something and tell you to head for the sewers and “Give this to Brecht”

And so, instead of Viridian Forest, you head for the sewers, where new Pokemon include Grimers, Glooms, a Poison/Dragon type modeled after squat; medieval-y dragons mixed with legends of sewer gators, Dark/Bug-type Cockroaches, and a very rare Nuke/Fighting-type terrapin that can evolve into four different forms; one focused on Attack; one focused on Special Attack; one focused on Defense; One Focused on Special Defense [COWABUNGA!].
The trainers you encounter would be hoboes who only have one; pretty high-level; Pokemon that you must switch out around a lot to wear down. Sometimes; in lieu of money; they'd give you items instead; including a fair few of the Leftovers.
Eventually, you go up to a very friendly sewer-village full of slightly-off-kilter weirdos and outcasts; learn more about the rebellious Team everyone's after; Team Rakuga; that they're anti-authoritarian but very much humanitarian; providing resoruces for the poor, but hated due to their attacks on the government. It is hinted though that the government itself is up to some shady shit and the police are brutal as hell.
And, in the sewer village, you meet the first Gym Leader, the Dark-type dude known as Johnny, a goth-type black dude (Think a mix of musician-Voltaire and Black Parade-era Gerard Way in fashion sense) whose gym is themed around disspelling fear of the unknown; with randomized puzzles meant to scare players but are easy to do if you approach them boldly.