Well I am sure we will see a use for the medals sooner or later. Remember Rainbow Medals ? No one knew what they are for in the first few weeks after implementing them.
Maybe they will be used as alternate currency for the Limit Break Dragon Nae chan (mofu :3), Considering that the Limit Break should be relatively rare thing for the most end game teams, and as such it should be fairly rare to do, it might be it. After all there are always multiple ways to get stuff in FKG, which is one of its best features.