There is lots of reasons really. Audience mismatch, the few RPGs the console got were really different than this, the inital revelation ans the final product are nothing alike and the fe connection is quite small at best, so even if there is an fire emblem audience on the console (which is not even a lock) they might not be interested on this game... Also, nintendo didnt even try to market the game in Japan, and considering its a new IP unlike something like xenoblade...
Its a shame. Looks like a great game to me, but its aestethics can keep some people away and i understand. People say the wiiu is a failed console and all and that's not a lie, having some games working hard to pass the 100k barrier, but when a game like this fail so bad, there is much more problems with it than just "its the wiiu". I guess its the same thing that happened with w101.