Alright! So here we are. 

Just so I can remind myself of Act I:
-Aria kills Lysa, Aria and Yerbol fight, discover a Star Map that leads to Quensu 
-Duo go into the temple, find all sorts of stuff, including crazy flying blind force beast (one of our favorite creations, honestly)
-Report back, Bracknell and Saresh form an alliance, start to colonize Force users.
-Tython and Korriban implode. 
-Retreat to Zinuthra after assembling remaining Masters and Lords. 
-Fight against Bracknell rages for months. 
-Finally Bracknell finds Zinuthra, launches full scale attack. 
-Aria and Yerbol slay Bracknell on his own ship with the dogs. 
-Peace (relatively) 

Act II: 
-Discovery of the Xiss and our favorite blue-skinned seductress. 
-All sorts of Xiss try to overthrow the newly minted government. 
-Eventually find where Xiss were created by True Sith, kill them, end of story. 

Obviously this is truncated, but just trying to capture everything the way I remember. 

How much change would you want to incorporate into the story? I've got a few ideas which I'll list in a second.

Edit: What I meant to say was: what do we want to do for the time skip? I'll get the ideas in a minute. I listed the events of Act I and II for later when we're ready to start that part of the story.