I'm picturing some sort of post-game sub-plot involving an exploration team discovering an "ancient Pokemon built for battle". You catch wind of it, explore the dungeon and find Genesect who you must then defeat. There will probably be some explanation as to how Genesect became the mechanical creature it is (May even reference Plasma, though doubtful).
As for Meloetta, there will probably be some cutesie little sub-plot involving a song or performance.
I'm actually not looking forward to the inclusion of Arceus :V I'm sorta hoping he remains as a "presence" rather than a recruitable Pokemon.