I think they should make an infinite phazon beam that you only get after you beat the game two times.
Hmmm… brainstorms*
Unlockables*
Survival mode infinite enemies attack you in a room, and they progressively get harder
Time limit hard mode* you have a specific time limit to beat the game, will be based on semi experts run throughs
Race to the finish* similar to SSB race to the finish, just enemies
Play as Metroid handler!!! (umm…mabye not)
play as Satoru Iwata!!! (awsome)
Mini mission* play as ridley*
end unlockables*
Lol, some of these wouldnt be that hard to do, and tons of fun. Anyway, i think that once the game is near completion, thes will come up.
Here’s my 2 cents…
Another hunter from Metroid Prime Hunters, such as Sylux. (I think Sylux would fit the role best)
A Global Federation trooper, but everyone else has mentioned it already 
A dark or normal Space Pirate Commando, which I’m suprised nobody has mention… cause that’d just own!
Reggie or Shiggy, expecially Reggie, so we can REALLY kick some @$$ and take names! Then the game would suddenly turn into something like Duke Nukem 2, where Reggie’s holding some large gun XD Morph ball could be handled like he just turns into his head XD