Found this from a random /vp/ thread you advertised, didn't bother reading much after the first paragraph in this page and just assumed it was a slightly fancier porn game, I was very much surprised to find an actual game with an actual story and actual characters.
I think this is really good, is a story that has enough of game lore, anime lore, and headcannon to not feel like either a boring simple story form the games nor a fan-fiction of characters with barely recognizable behavior. I feel Cynthia and Jasmine's traits have been amped up to eleven, but I'm not sure that's a bad thing.
Overall I think you made something real nice, with enough options to make this feel a bit less linear but still tell a straightforward story.
There's only one issue I felt could be a quick fix, even though I know nothing of game design: The MC showed their partner pokemon to Cynthia twice, the second time happened even after it evolved, tried to be vague to avoid spoiling anything for the people that may think that's a spoiler somehow.
Also I'm not sure about the sprite for Shawn, might have to use another one form the games? Don't wanna shit on your photoshop skills but, you know, at least I appreciate you changing the color of the helmet of the totally random mundane engineer trying to fix the backup generator, that's a nice detail.
Right now I've only seen one ending but I wanted to give my feedback while everything is fresh in my head, but I'll try and get all of the endings and explore all the dialogue options I've missed, If I wanna add anything new I'll post it after.
Up until now at least, I can say it was a lot of fun, thanks for taking your time doing this!