Thought I might spark a conversation even if I'm probably the least qualified to start this conversation in particular... but what do you think will happen in Metroid Prime 4?
As I've only played the first one, I can't give any speculation worth hearing, but if you must know... I think Dark Samus will resurrect and team up with Meta Ridley to kill Samus alongside the Space Pirates in an unexpected survival horror twist on the series.
Now that I'm done, discus! ...I hope there are better ideas to look at by the time I finish the trilogy and check this thread again.