The base idea of federation force wasnt a bad one. It was everything surrounding it that was shit (thanks tanabe).
I always envisioned the base idea of that game (even before federation force was shown) as a game placed after Fusion and before the next main game. Were 4 soldiers from the galactic federation, all with their own personalities (so real characters, two female and two male characters would be great, in fact, make one of the female characters the leader of the team, so it feels very metroid) have the mission ofn going after Samus hrough different planets to capture her. At first the team is all for the federation and are sure that Samus was in the wrong and should be aprehended, but during the game theyb will discover the harsh truth of the real hero Samus is and how the GF is corrupted from the inside. Samus appears in the game and at the ends saves your ass basically, and when the time comes to caputre her because she is defensless in some way (because of a monster she was going agaisnt or whatever) the team decides to let her go.
The game could be played in singleplayer with the CPU controlling the other 3 characters, or multi player in a coop op adventure with shooting parts and puzzles (so more metroid Prime and less Halo, but a little more actiony than normal metroid with some big setpieces and a little bit more story driven).
Its a good spin off also to build an actual sci fi multiplayer FPS game for Nintendo were teams go against each other without trying to force it into real metroid.
Theres also a real example of this game with Star Wars Republic Commando (though it should be done much better than this one, and with actual interesting and charismatic characters, because the ones in Republic commando, phew....). That game actually drinks a lot from Metroid Prime
I would also add this. This game would be much more welcomed if people knew a real Metroid was coming also (so never do what they did with Federation Force again) and that having all the more dirven story and multiplayer aspects in this spin off will have the real metroid keep being classic and intact, like Samus Returns was and hopefully how MP4 is.
In fact, putting it between fusion and a new game would make people clear Sakmaoto wants to continue with that story (that we already know thanks to the ending of Samus Returns, but this would help explain the GF corruption and them chasing Samus without touching so much the main games).