If you scan any non Metroid amiibo into Federation Force, you will receive a custom skin on your Mech based upon that amiibo in the multiplayer mode, Blast Ball.
Nintendo also said in a seperate tweet: If you scan a Metroid amiibo into Federation Force, you will receive an upgrade for your Mech during campaign missions.
Nintendo has yet to say what the upgrade does, but it appears that it makes your Mech bigger.
Metroid Prime: Federation Force will be released on August 19th for 3DS.
