EDIT: and the emperor isn't going anywhere. they might reveal who he really is, but he isn't going anywhere
They reveal who the Emperor is in the Revan novel - it's a quick, decent read that also ties up the KoTOR 1 & 2 stories and sets up one of the TOR companions as well.
Future story lines:
I'd like to see the Sith Inquisitor and Warrior really turned loose on the Republic. It made a lot of sense for their stories up to now to be based on in-fighting/betrayal given the Sith's nature, but now that they're secure in their positions you could see them taking the fight to the Republic.
SI: As head of the Sith's arcane knowledge branch s/he could discover a weapon from the first war against the Republic (like Naga Sadow's sun-destroying ship), recover it and use it to attack the Republic. It'd be a pretty epic Light/Dark choice to get to decide between wiping out a planet/system to show your power vs sparing them if they surrender to the Empire.
SW: Could be sent to assassinate members of the Jedi Council to try to balance the scales after there's been so much upheaval in the Dark Council.