Here's what I want to happen:
The Empire gets new leadership through bloody takeovers and inter-fighting (it's expected of the Sith). The new Dark Council then decides to make sweeping, but popular reforms which will allow aliens to fully join the military and Sith, rather than some rare cases like the SI when he/she starts out on Korriban, go on the offensive against the Republic, actively seek out new allies to aid them in their struggle, and others like that. The Empire would then conduct many military raids and attacks in several sectors, which would spread the Republic army and navy thin, and Sack Coruscant (PROPERLY), burning it to ashes and leaving no survivors.
Unexpectedly, the Republic armed forces, along with the Jedi, would fight back so viciously that the Imperial Military would be pushed back, and all the territory they gained would be taken back until the Dromund system and its close neighbors would be all that's left of the once great and mighty Empire. The entirety of the Imperial Navy, Army, Sith Order, some of the Chiss Ascendancy's forces, and all Imperial Intelligence personnel would regroup on Dromund Kaas for a glorious final stand. The battle would be EPIC BEYOND ALL MEASURE, with the Imperials making the Republic pay for every single inch they took. Eventually, their numbers would be whittled away, as the Empire's numbers were never as great as the Republic's, until the Dark Council and all leaders of major military branches would make their stand in the Imperial Citadel. Fighting like Sith Spartans, they would fight to the last man, woman, alien, and droid, until at last, the remains of the Sith Empire, which had lasted for almost 4000 years, would be finished.
The victory would be so costly that the Republic would take centuries to rebuild, making it a Pyrrhic Victory.
THAT is how SWTOR should end.
This, pretty much. Maybe not the total destruction of Coruscant, (because I doubt it could be rebuilt in time for the movies) but otherwise pretty spot on.