I think, now that we've moved into 3D games and carts with much more expansive memory, that they should introduce slight appearance variations that can be passed down via breeding. Shinies stay the same more or less, but there should be small appearance differences within species, probably 3-4 depending on the species, maybe more if it makes sense for flavor.
i.e. Charmander line can be found with normal skin, striped (think the clones from the first move), or speckled ala Bulbasaur. Meowth can be found in a siamese, calico or tabby pattern in addition to its normal form, with corresponding shinies (siamese becomes a tuxedo cat, etc.)
Kecleon should be available in numerous shades depending on where it's egg hatches, or some other environmental thing, with the stripes being what changes color in shinies. Breeding a kecleon with good stats and hatching it to be red/purple would be really cool.
That alone would make the game much more fun for me, just trying to acquire all the various cool forms available. And let's be honest, Tuxedo Meowth in Amie would be fucking ADORABLE.
