>>32723966I mean... it's literally the same as the same breed of certain animals having different fur colors in real life. Dogs, cats, horses, rats, etc. all are the same exact animal, but can have colors that run the gamut from pure white to orange to black and lots of variations in between. The only reason I can see for shinies being so rare is that pokemon physiology, being so different from regular animals apparently, is just stable enough that variations are practically non-existent, and shinies are simply the product of extremely recessive genes and/or mutations, much like the spiky-eared Pichu.
That said, one of the biggest things I've always wanted to see in a new pokemon game is some kind of "traits" I suppose, similar to Vivillon, but all (or mostly) available in one game. Like a small handful of similar shades for a particular pokemon, a few patterns and one variable trait per pokemon. Like a charmander could come in a few lighter and/or darker shades of orange/red, with either standard skin, some kind of chameleon-esque stripes or splotches like bulbasaur, and his tail flame could be regular, intense or small. Make these traits breedable and you'd be able to customize pokemon to your liking, so if you're not fond of Blastoise's coloring, find a squirtle that's a brighter shade and breed it with the pattern/trait you want to get a more vivid Blastoise with a cool look to it. It wouldn't exactly be hard to do since it's mostly texture and effect work, it would just take a bit of doing to implement on all the existing pokemon. It'd make shiny hunting a total bitch trying to get the right trait/pattern *and* shiny though.