Like I said, philosophically, Republic/Empire and Rebel/Seperatist makes sense. One represents the established government and the rule of Palpatine. The other represents the revolutionaries fighting against that establishment.
But at the end of the day, the PT and Clone Wars still clearly portray the Republic as the good guys and the protagonists.
If you think FFG is really going to put the faction with all the Jedi in it in the same faction as the Empire, you're crazy.
Also, nearly every Clone Wars republic ship looks like it belongs with the Rebels. Clone Y-Wings, clone Z-95s, the ARC-170 looking like the X-Wing's prehistoric ancestor, etc.