Well... The reason is probably that no publisher thought Japanese gamers would buy it. Another is that the title's violence might have problems with the censors.
Even if the game got an 18-and-up rating, the gore would need to be dialled down a few notches.
The reasons why the title is prohibited in Japan is being discussed over at Japanese site Ameba News. But what do commenters on the Japanese internet think the reason why Wolverine won't be released? According to 2ch:
-The sad fact is that games in Japan dont sell unless they have Moe characters -Is this game actually selling well overseas? -No its because games from films usually turn out rubbish -Games that have characters made of Lego do well over there - is that some sort of game you want to play? -Games overseas give me the impression that its all kill -Well if they called it "Se-x Men" instead and had tentacles instead of claws then it will probably do well here -Well how come they release Ninja Gaiden2 in Japan which is full of slashing? -Well Japanese only play RPGs -Japan is tough against grotesque expression while the west is against ero - how has it become like this? -But Japan is full of eroge. Japan is after all an ero country - brilliant!