Pokemon Factions

-All Pokemon up to to Gen 6 obtainable.
-A darker world
-Faction system (4 Factions, Join one, some others turn against you)
-4 Legendary fakemon (One for each faction, these will be the only fakemon in the game)
-Special abilities instead of HMs
-A pokeball maker who can even craft masterballs for the right price.
-All new, large island of Kibo
-And more..

Starly
(I'm open to suggestions on this)

-Neo Druids (Grass/Rock types, special herbs, )
A Faction of druids following the ways of old. Kibo has been their home for as long as anyone can remember yet they do not easily associate with outsiders. They will be hostile if the player invades their territory until you save one of their members from a Synth Soldier lab.
Legendary Pokemon: Eponya - (Grass/Fairy) This legendary Pokemon is said to embody the spirit of an ancient goddess. It resembles a horse and can to run on air. If exposed to an ancient stone after bonding with it's trainer it assumes it's true form.

-Dark Soldiers (Steel/Dark types, synthetic potions, )
Soldiers who care about nothing but pushing the boundaries of Pokemon and human ability. They are said to take part in terrible experiments and are the reason that Kibo is decaying due to pollution. They are relentless and are likely to attack the player on sight until he impresses them, which leads to a choice to join their faction.
Legendary Pokemon: Project Gen - (Bug/Steel) After hearing that a Genesect was revived and modified by Team Plasma, the Dark Soldiers decided to do the same, but decided to do the same, but pushed the modifications to an inhumane level. This tortured creature is currently kept deep below the Dark Soldier HQ where they hope to gain control of it one day. A scientist has detected strange new cells in this Pokemon's DNA, indicating that it might be able to reach a new evolutionary form.

-Pirates (Water/Poison types, Alcohol, )
Pirates need no introduction. These foul mouthed, rum loving scoundrels can be found on beaches, on their ships and their outposts scattered across Kibo. They are murderous and greedy, but not without code. Prove to them you are worthy and they might let you join their ranks and reap the benefits.
Legendary Pokemon: Kraycaan - (Water/Poison) The Pirates of Kibo believe in a beast that lives in the deepest reaches of the ocean, able to shift it's size, it is powerful enough to swallow ships whole. Thousands of years ago the beast was said to be trapped in it's smaller form using powerful voodoo, someone skilled in this same art may be able to restore this Pokemon to it's former self.

-Enlightened (Psychic/Ghost types, gifted abilities, )
The Enlightened are probably the strangest faction on Kibo. They will not attack you until you partner with another faction and will assist you throughout the prologue of the game. They are a group of "gifted" people, all possessing special abilities such as telekinesis, suggestion, etc. They seek an ancient creature that they believe could repair Kibo and save it's people, though many call them crazy. They will recognize the player as "gifted" and can unlock your ability if you join them later in the game.
Legendary Pokemon: "The Nameless" - (Psychic/Ghost) The enlightened revere an ancient entity they call "The Nameless". This Pokemon was said to be similar to Giratina, yet no mention was made of it in Pokemon history, many call it a myth while others claim to have seen it.

You start in a little town called Mona. It's dark and stormy outside. You are only 12 years old. You hear a knock on the door, your mother runs up stairs, telling you to hide under the bed and to stay
there. You hear screams, followed by someone coming up the steps. A Synth Soldier comes into your room and looks around before heading back down, then the door then shuts down stairs. Terrified, you run down to find your mother, covered in blood, telling you to sneak out and run as quickly as you can, she prepared a plan in case this happened, the Enlightened will help you get away. You cry, but your mother smiles and says it's alright, you just have to be strong now. She tells you to take the back door and grab the running shoes on the counter.

Outside you stumble upon a heavy bag of Pokemon that seem to have been captured by the Dark Soldiers. You grab the first pokeball and start running through the tall grass to avoid being seen. (At this point you receive Starley. Leaving the grass will put you up against soldiers with lvl40 Pokemon)
-I've considered having Starley be found in a trap behind the house instead, having you save her, after which she helps you.

You find your way to the beach, where you hide behind some washed up driftwood. At this point a woman runs up behind you, you try to run, but she stops you, Starly attacks her but fails. She tells you to calm down, she is one of the Enlightened and she knew your mother. She tells you that you have to get to her raft. She calls out Drowsy who promptly puts some of the nearby guards to sleep. She then follows you. You run across the beach and reach the raft, she cuts it loose and you climb on it, she is then captured by the Dark Soldiers as you are drifting away.

You wake up on an unknown beach while Starly is pecking at you to wake you up..