I remember a lot of advertising for Metroid Prime 3. After all, it didn't pull a 300k launch in America out of a hat. The reason Metroid isn't a big series is simply because it's too niche to appeal to a large audience like most other Nintendo games. Although some people would hate to admit it, a masked and silent hero in a sci-fi world has never been the perfect way to snag the Nintendo demographic (it doesn't help that the franchise isn't your typical shooter). Characters like Mario, Zelda, etc. have been so successful because they managed to appeal to everyone, from the youngest kid to the most battle-hardened fanboy. Metroid doesn't have that same type of appeal, and its popularity is shrunken by the more popular series. After all, why isn't Pikmin a bigger series? What about F-Zero? What about Yoshi?
'Sides, I think Metroid Prime was bundled with the Gamecube for a short while (explaining the high sales).
