Hopefully the war between the Sith Empire & the Old Republic will last something like 2000-3000 years (1k before the movies), o we may yet to see differents "evolutions" between the two parties.
I would prefer that it ended within our characters' lifetimes. It would be nice to see that the heroes that emerged after the Treaty of Coruscant successfully ended the war. Nevertheless, it wouldn't make sense for the conflict to last until 1000 BBY--it is established as is that a separate Sith Order rises against the Republic in 2000 BBY.
We have no proof of that - it's actually quite likely that the Republic and Empire somehow merge. After all: During the clone wars, the Republic symbol is the Imperial symbol from this game.
Daniel Erickson, the SWTOR lead writer before leaving BioWare, mentioned that an eventual merge will occur that brings Imperials to the Core Worlds and would explain how the Imperial accent thousands of years later is known as being the 'Core' accent. I would assume the Imperial insignia-merging would occur as well.