You know what would have been better?
If they really wanted a Metroid with multiplayer, this is how I would have handled it.
The single player would be a standard Metroid game. You play as Samus, blah blah, they give you tons of control schemes, and everyone is happy.
Now with the FPS multiplayer, I would dump Samus out of the picture and focus on the rest of world of Metroid. You pick which race you want, Humans (Galactic Federation soldiers) or Space Pirates. Maybe even throw in more races if time permitted (Chozo, Luminoth, Ing). The Humans/Pirates thing is actually a lot like how the Human/Elites work in Halo. Anyway the humans would have their own weapons, different types of soldiers to choose, their own vehicles, etc. Same for Space Pirates. The game would play like an FPS. Tons of options for customizing your multiplayer game. Imagine an 8 on 8 LAN mayhem humans vs. pirates game, anywhere you want. Say, after school before [band, football, whatever] practice starts. And you wouldn't have all the crazy "hardcore" fans screaming about desecrating the Samus legacy stuff.
I hope FPS's become common. I'd love to play Timesplitters, Halo, Unreal, or whatever in random places when I'm bored. And Halo is entirely possible since Microsoft has no problem in having its games on GBA, and if Bungie is like ever other developer they will probably go nuts at being able to make games for the DS.