Wow, um this is pretty nice.
The story is great, kudos for that, the pokemon sprites are pretty good, but I would like to give you some critisism.
This sprite looks adorable, though you overshaded it a tad, pokemon shading is pretty simple, try cleaning it up a bit.
I rather like this one, the stomach should have a lot more shading though, also work on the legs.
Again, you kinda overdid it with the shading.
The title screen looks pretty cool, good luck putting it in game :P
Lesten the palettes a bit, it'll be easier to insert.
Last peice of advice, try to learn how to script, XSE is one of the easiest and most versatile script editors out there, scripting is needed to acheive your vision,
https://www.pokecommunity.com/threads/164276
That's one of the best tutorials out there, please try to learn.
I hope to see your game blossom :3