I have a lot more, but its all spoilerified. Is this too dark and gory for a pokemon game?
I think Pokemon could stand being made 'darker and edgier' - I mean, Pokemon battling is essentialy similar to dog fights. But you have to be careful in how you do it, or you enter cliche land.
First, everyone knows that ANIMAL CRUELTY IS BAD. That shouldn't be your story's main focus. It's almost redundant. If your plotline involves the protagonist chasing after villains who mindlessly torture innocent fluffy creatures, there's no value in it. The trick is in finding something ambiguous in it, something with two sides. For instance, the fine line between 'Pokemon cruelty' and 'Pokemon as working animals'. You could show the transition in stages: dog-type Pokemon being used for hunting, dairy Miltank being kept in crowded conditions, Rapidash being whipped, Ursaring at the carnivals, Torchic in rooster-fights.
Second, there's the issue of Pokemon battling as being rather cruel. If you leave it out, the gameplay collapses, but if you don't explain it in some way, the player is sure to notice the double standard - so it's wrong for the villains to keep Pokemon in small cages, but alright for the hero to keep them in small balls? And isn't it wrong to make Pokemon fight each other for sport?
Third, there's the cliche around abused Pokemon that they will form an immediate, super-strong bond with their rescuer. In fact, the most logical thing for it to do when released is high-tail it into the forest. Why should it expect anything good from you?An abused Pokemon should have a fear of people and take a long time to get used to being handled by an owner.
So...I don't really know. I'd like to hear the rest of the storyline, though.