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.
because we all played the games and read the books right?