Metroid Prime: Federation Force is not looking like it is going to get that much attention from game players, but still is trying their best to provide attention to the game with a new feature they have announced today. Metroid Prime: Federation Force will include amiibo support as revealed through Twitter by Nintendo, they shared a handful of images which showed how amiibo's will be integrated although it won't be for anything special.
For the minigame mode Blast Ball Nintendo shared examples of amiibo usage with Mario and Bowser, wherein these amiibo's will give your mechanized robots some new coats of paint based on that amiibo. Mario and Bowser are the only examples given, but I feel it would be safe to assume that various amiibo's will offer the same in game affect.
Nintendo has also revealed how amiibo's will impact the story mode, and these are a lot more precise. You can scan the Samus, or Zero Suit Samus amiibo's and these will grant you special bonuses to help in missions, they will also change your characters color to match the amiibo, so hey Samus is in the game then.
Metroid Prime: Federation Force is expected to arrive on August 19th, you can find Nintendo's amiibo examples below: