This is basically the number one reason I want Gamefreak to move to a console format. More data storage available and the capability to implement something like this. There really needs to be different regional variant forms of pokemon if nothing else.
My dream come true would be if each pokemon had 3-4 variable "traits" like horns, pattern, color, tail, eyes, etc. with each having 3-5 variations that could all be selectively bred for.
Each pokemon would come in various shades of its standard color, i.e. Marowak appears standard in shades of Yellow to orange, with maybe a few errant shades of red as a rare variant. Shinies come in crazy shades attached to each variant color. Standard Marowak shiny is green, but a lighter shade of orange becomes blue when shiny, or a darker shade may be pink when shiny. Gives you a lot more options and element of surprise.
Combine that with various patterns (i.e. Standard Marowak, one with stripes, one with spots, one with color points), traits (spiny marowak, ridgeback marowak, scaled marowak) and other variable traits (maybe marowak can come with a longer/shorter tail, or have a club on the end of it, or perhaps spikes) and you'd have some extremely versatile appearance options.
It'd add an element of fun to breeding as well, since you'd have to start off breeding for stats or appearance and when you've got the right traits isolated, breed until you get the perfect match of ideal stats and coolest look.
I would gladly throw money at Gamefreak for a game like that.
