I think anyone that's a fan of the YouTube show Game Theory had to anticipate this one being brought up.....
Watch the video. No real way to abridge it. Anyway in regards to everything said: Mind=Blown.
If you stop to think about it the theory actually DOES make sense. Not only does it cover the lack of certain Pokémon in other versions, it also covers several other things as well:
-The difference in villain team in Ruby/Sapphire
-Lugia/Ho-Oh's locations in Gold/Silver
-A potential storyline reason for additions/changes from generation to generation ("discovery" of new species of Pokémon, addition of Mega Evolution, ect)
This image also helps break things down if you really want a TLDR version of the theory:
Anyway thoughts on the matter?