Interesting idea, one thing I noticed is that the technology wise the period of the Great Galactic War seems to be far more technologically superior to that of the New Sith Wars. Observe, New Sith Wars - very archaic looking, more akin to the the technology of the Great Hyperspace War or the Great Sith War (infact even more archaic looking). Then we have the Great Galactic War period A lot more modern looking right? More akin to battle scenes from the Clone Wars. So surely there must have been some sort of devastating catastrophe that plunged the galaxy into some sort of 'Dark Age' over that 1000 year + period. The mutual destruction of the Sith Empire and the Republic could be that catastrophe. But for various technical reasons I doubt we'll see it ingame, more likely in some form of novelisation. But this would leave room for the Emperor's final death (if he's not basically dead already) as infighting would tear the Empire apart.
How I'd love TOR to end would be Republic severely weakened. Many systems withdrew from it or were conquered by the Empire. And before the ultimate blow is done the Emperor dies (by who, though?) and the Empire splits into various "kingdoms" and "states" of which some are also joined by the Republic separatists. It wouid be good imo because there would, finally, be no huge dominant super-government ruling the galaxy.
Players could be left assigned to the remnants of the Republic and one of the new Imperial remnant faction, which controls the original Sith space.
It's plenty of time before Ruusan reformation and all Darth Bane saga.
There were questions raised to how the Empire would look like after Emperor's death. Here is my suggestion. Many smaller, independent sectors instead of a huge territory ruled by a single government. But then Republic would have to be appropriately weakened :l
It would be reasonable, Republic is properly bashed (But not so dead yet!) and there is little left to fight for, Emperor dead and many Darths aspiring for the title, let the power and territory grab begin ^^
Then again, the destruction of the Republic could send some serious tremors through Star Wars continuity...