Coming from a Eurogamer interview with Nintendo's Kensuke Tanabe...

"[Metroid Prime: Federation Force] is an attempt to expand the Metroid universe. As you can play with up to four players it wouldn't make sense to play as four Samus characters! The game will be focused on co-op, working together as a team with up to four players. And obviously it is available as a single-player experience as well. You have the option to choose load-outs for you to bring to the battle. However, you have to consider that there will be limitation for how much can carry as a character. If you carry the Super Missile then you're classed as a Warrior type. If you have lots of Repair Capsules you could focus on being a Healer type.

I've always been thinking about having a battle between the Galactic Federation and Space Pirates. The Metroid Prime series fits between Metroid 2 and Super Metroid, as you may be aware. So it falls under that same timeline, but looking at it from a different perspective. You may be able to see Samus in the game...

It's set on a planet which the Galactic Federation used, way back when. The plot involves a struggle to retake that planet. You find out that Space Pirates now reside there and are building a weapon to use against the Federation. Players will fight the Space Pirates to stop them.

Ideally I thought this game might be released around the same time as the New 3DS but it got a little delayed... It was begun around the time that I learned that the New 3DS was in development due to the inclusion of a C-pad, which would be perfect for an FPS."