Wait, really? Why would they do separate versions in Japan but put em together in one game for the rest of the world? If that really is the case that's great, but it sounds a little odd. Just as long as it's not some eShop only ****. I don't have the space for a whole game on my SD card.
It seems that Japan might be getting the short end of the stick in that regard. It could be Nintendo trying to monetize the vastly more prevalent popularity of the fire emblem franchise in their home country...
Fire Emblem has always been much more popular in Japan than it has been in other regions. Awakening was the first massive step forward for the franchise overseas, being the only fire emblem game that received massive popularity pretty much world-wide. Of course their were other Fire Emblem titles released over here to a very positive response, but I can say with absolute certainty that none of them reached Awakenings level in popularity.
This is the next game after Awakening and while Nintendo are very confident with the popularity Awakening received over here... it seems to me they don't want to push their luck.
Basically, I think they're only selling two versions in Japan because Japan is the only place where Fire Emblem is popular enough for them to feel comfortable with selling two versions. In Japan, both versions will sell, they'll sell very well and Nintendo knows this.
Over here however, while Fire Emblem is popular... the conversations displayed so far show pretty well that we would not be happy with two different versions being released simultaneously. Nintendo know this as well.
Pokémon doesn't have this problem because it's a damn near world-wide phenomenon, Fire Emblem simply hasn't reached that status yet and may never do so.
That's my take on it anyway. If this game is as popular as Awakening was over here... and if the two version strategy works very well in Japan... then you can take my prediction that the Fire Emblem to follow "If" will be split into two versions for us as well. (Assuming that it isn't just a one time gimmick for "If" that is.)
In the end would it really be that bad though? If we got our Fire Emblem games in double packages from here on out? Each representing a different side of the in game war presented? Who knows? Regardless, I think thinking into the games following this one is a little too prediction heavy, so for now just take the two version plan as a way for Nintendo to make more money without pushing their luck.
But in the end? That's just a theory. A GAME THEORY. Thanks for reading.