Yeah, who knows. Maybe you're each a metroid of different colors and you are unleashed on a planet, and you have to compete to evolve the fastest, or see how many kills you get before you get blasted. Since you evolve based on how much energy you absorb, it could be fun
Or perhaps they could do something like the Pac Man game, where one person is Samus and the other 3 are Metroids wreaking havoc on a space station.
You could also all be space pirates, perhaps rogue pirates that are fighting against the main space pirate bunch for some reason. They've been marked for death and have to fight their way out. You could do some co-op stuff that way, too.
I like what Nintendo did with the Pac Man game, and I hope I see more multiplayer games, online and offline, that do similar things. There are already "king of the hill" gametypes, but it's just not the same when anyone can be the king.
edited to add: Didn't Metroid 4 end with the realization that there were a dozen or more SA-X clones? Given the inclusion of the Fusion suit in Metroid Prime, it wouldn't surprise me if they included SA-X clones in Prime 2's multiplayer.