Hmm... maybe there could be a Spinda-type system implemented where each Pokemon would have some sort of individual markings...
I've always been extremely frustrated by how little advantage the Pokémon developers take of the potential for intraspecific variation. It would be so simple to do! I wrote a little program to do that myself a few years ago (I keep meaning to make a web-based creature-breeding/raising game based on realistic genetics, but never get around to finishing it). At the very simplest they could just modify palettes based on some IV-like value; even that would add a great wealth of diversity and personalisation to the game.