To me, it left more questions than answers.
Spoiler Alert!I heard that it was Sylux's ship. I haven't played Hunters, but I know that he is a being that detests the Galactic Federation. Maybe the backstory will be explained in the next game. I speculate that he was watching Samus and the other hunters ever since the conclusion of Hunters all the way into Corruption. This will obviously lead to a sequel but it may be during or after the Prime story arc. It may lead to the multiplayer that some fans have been bitching about for so long, but I hope that it's a Wii sequel.