A new Metroid game has finally been announced for 3DS. It's called Metroid Prime Federation Force.
Very little is known about it, but based on the teaser trailer revealed during Nintendo's E3 presentation, it appears to support four-player co-op and looks to be set in the Metroid Prime universe.
There also seems to be a three vs three mini-game called Blastball.
Metroid Prime Federation Force isn't due until sometime next year.