I have to say, I really like the character design and spritework that is presented here. The protagonists look cool, the satanic cult actually looks like a cult, the two "jerk" characters make me want to punch them just by looking at them. On top of that, you're giving just the right amount of info on the story, without typing entire paragraphs of confusing backstory and that makes me actually want to find out about the story myself while playing through.
The Fakemon are... fine. They're not bad, they're very well sprited, I just feel most of them have very complicated designs and wouldn't fit that well alongside the official Pokemon. Another minor nitpick I have is about the tilesets. Some of the tiles - particularly those taken from other games - have way too dark outlines, compared to the rest of the tileset. Maybe you could smooth out the colors a bit, in most cases this would require just some minor pallette edits.
Overall, I'm a fan of this project and I'd like to see how it develops. By any chance (and I'm in no way pressuring you, because I understand the ridiculous amount of work that goes into making something like this) are there any plans for a Demo/ Beta yet?
EDIT: Never mind. I just realised this has already been answered. Keep up the good work!