Most likely cultural differences. Metroid draws heavy inspiration from Alien, and other similar series', which are all western.
I don't think it's that it does bad in Japan, it's just because of the inspiration from such sci-fi series', that it simply does better in the west, because I think we can all agree that we love sci-fi and "space adventure" stuff in general (Star Trek, Star Wars, Alien, Starship Troopers, etc).
So it's more to do with the fact that we simply love it more, rather than it just being Japan not liking it.
Official Dick Gumshoe of the Ace Attorney boards, pal!