In a recent interview with USGamer, Metroid Prime: Federation Force producer Kensuke Tanabe stated that he has thought about including Amiibo functionality in the game.
According to Tanabe, he has "a few ideas" about how Amiibo could interact with Federation Force, but he can't say anything more currently because nothing has been finalized; he also stated that he would like to have an Amiibo of Federation Force's mech. Here's Mr. Tanabe's full statement:
USGamer: What happens if I’m playing on the New 3DS and I take my Samus Amiibo and tap into the 3DS?
Kensuke Tanabe: So while I do have a few ideas, I can’t quite tell you at this time since they’re not all finalized, but there are some ideas coming. If possible at all, it would be nice to have an Amiibo of the mech.