My Illogical Theory
In X and Y, they probably did this because they are aware at how much you want that damn shiny, and so they gave you a chance. With the 3DS, they thought that it would be practically impossible to access the hidden data, therefore they wanted everyone to think that the shiny chance was still 1 in 8,192 but increase the chances of getting a shiny so they can make you feel better about yourself. xD
They probably took this into account - they probably wanted you to have a better chance of getting a shiny so you can do something else with your life rather than sit in front of the 3DS and hunt for that damn shiny Pokemon. :3
In Gen IV, it says on Bulbapedia's Masuda Method page that Junichi Masuda may have added the Masuda Method to encourage use of the GTS. It can't have been a coincidence that the Masuda Method and the GTS were introduced in the same generation, no?
Also, there are rumours that state that the Friend Safari has an increased shiny chance. If this is correct, they may have increased it there to make you get shiny Pokemon of non-native Pokemon, which would be great!
So yeah, that's my theory. :D
Hope I helped. :)