Ok, roll with it. I know that Nintendo would never do it.
There should be a major reform in the breeding departmernt. You should be able to obtain different colored pokemon through breeding. Sure this might render shiny pokemon useless, but think about it. You would be able to obtain every pokemon in nearly every color (save unbreedables and legendaries.)
For example, the ever popular HSOWA thingy. You'd either get a blue skitty or a pink wailmer. You could breed the blue skitty with a pikachu to get a blue pichu. And so on.
Sigh, pipe dreams. Anyone else have any completely ridiculus ideas that would nonetheless be awesome, although would never happen?