Just a quick tip:
Whenever you make any pokemon, it should automatically make a shiny version, using a separate (already made) pallete. This can be a blessing (because you dont have to make two copies) but if the pallete is completely different, you can run into graphic problems. Of course, actually finding a shiny pokemon is so rare, that it wont really affect you.
Other than that, good job (y)
EDIT: Also dont forget to edit the mini-sprites that are found when shifting pokemon, or else theyll be the originals and mismatched.