I think Sqrl is on the right track with the "maiming" comment. Metroid, although it looks like an FPS and plays a little bit like an FPS, does not deliver typical FPS gameplay, at all.
Some may recall that when Metroid Prime came out there was a huge advertising blitz and between Metroid and Resident Evil 0, GameCube outsold Xbox and came quite close to matching Playstation 2 sales for November of 2002. Then Metroid Prime 2's sales were very disappointing...why? I believe people bought Metroid Prime, played it, and didn't like it because they were expecting more traditional FPS gameplay. I even know one person who did just that - he bought a GCN for Metroid Prime and after trying it once or twice, never touched it again.
That's just anecdotal evidence, but I really believe that, like Sqrl said, people look to FPS for shooting, not puzzling and not adventuring. They don't want to scour a huge open world for secrets, they want to go from point A to point B. They don't want lock-on, they do want 20 guns that get more and more powerful. They don't want to roll up into a ball, they want to pilot tanks and space ships. They don't want scanning, they want to shoot stuff in the face. They'd also like to have Co-op and deathmatches, but as someone else pointed out, those can be optional if the single player mode is really good.
I'm oversimplifying here, but the point is, Metroid really doesn't play like your basic FPS, and I think that kills its popularity and also stops people from comparing it to other FPS games. Nintendo's lack of marketing and the GameCube's general lack of popularity didn't help either, but like I said, Metroid Prime was a system seller and Prime 2 was a (relative) flop.
