Up until the release of the Xbox, almost every successful console in modern times had been made by a Japanese company. Microsoft became the exception with their Xbox series of consoles, which was a hit everywhere except
you guessed it: Japan. The Xbox 360 has been doing slightly better, due to games like Final Fantasy XIII, but the original Xbox would routinely sell only hundreds of units a month. In a country where gaming is one of the most popular forms of entertainment, those are N-Gage numbers.
First person shooter games are extremely popular in the U.S. and they're almost all made by American developers. Perhaps it's our cowboy roots, but Americans just enjoy shootin' things more than the Japanese do. According to a poll by Japanese gaming magazine Famitsu, the prevailing opinions on First Person Shooters include "I don't think I'd be good at it," and "I don't see what the point is."
I always just assume every Nintendo franchise is a success everywhere, but it seems this isn't so. This could also explain why it took so long to get a proper sequel after Super Metroid, and why that sequel happened to be by a studio in Texas. It's weird to me that this franchise didn't really take off in Japan, because the movie Alien was fairly popular there, and Metroid is the exact same thing. It should be noted that the franchise has done much better lately, with the release of Metroid: Other M. Yeah, you know the one that's nothing like the series, for the worse? That's the one that does well.