Personally I think it's because they realized that doing it the way they used to gave a good number of people the amazing idea to sit in front of a legendary and reload the game for hours on end until it was shiny (and/or had great IVs). Parents probably noticed that their kids were droning away with their Pokémon games and it was bad publicity.
Seems like random conjecture at first, but if you consider some of the other changes that were made, like simplifying shiny hunting, adding shiny breeding shortcuts, giving you better O-Power regeneration if you stop playing and take a walk, guaranteeing some perfect IVs on Pokémon that can't be bred, greatly simplifying EV training, etc etc, it becomes pretty apparent they were trying to distance themselves from the impression that their games cause children to stare vacantly onto a screen, and to reduce the time children actually do stare vacantly onto a screen.
And like Javelin said, the likely reason those unobtainable shiny versions were put in the game anyway is to prevent crashes if some fancy hacker figures out a way to make their legendary shiny and forces the game to call data that wouldn't exist if it wasn't put it in.
