It has been discovered that the Metroid amiibo released for Metroid: Samus Returns also works for the previously released Metroid Prime: Federation Force. By tapping the amiibo on your 3DS in that game, you’ll unlock two Metroid-themed Paint Jobs, Flying Life-Form in the Campaign, and Floating Parasite in Blast Ball. The Campaign Paint Job lets you carry packs of five Repair Capsules instead of only one, but Blast Ball Paint Jobs do not give gameplay benefits.
Apparently, dataminers found references to a Metroid Paint Job a while ago, but it was not usable until now. This means that the Metroid amiibo has been planned for over a year and secretly implemented into Federation Force. The Samus Returns Samus amiibo does not do anything different; it unlocks the same Paint Jobs as the Super Smash Bros. Samus amiibo.
Source: Hyrule Blog