How I'd do it:
Keep Sith, Jedi, Scum and Villainy, and Smugglers and Spies. Add Republic and Separatist Confederacy. To avoid having too much disparity between the four "timeline neutral" affiliations and those introduced for the prequels, there could be a big ol' boxset with an emphasis on the latter, sort of like they're doing with SnV and SnS in the Edge of Darkness expansion. When they introduced the Order of the Silver Twilight faction to Call of Cthulhu: The Card Game, when that game was already rich with material for its seven existing factions, they compensated by weighting the next cycle's content towards the new faction in order to bring it up to speed, along with the fact that a lot of the Silver Twilight's early content emphasized "splashability" that made it worthwhile to include in decks that focused on a different faction. They would likely need to do the same thing here, but the task is made trickier by the fact that the new affiliations would be divided from existing ones by the timeline itself. To keep the Rebel Alliance and Imperial Navy factions from falling behind, any Force Pack cycle that deals with prequel material should also visit the early days of Palpatine's New Order, as well as the first sparks of rebellion. Since the game already takes a relaxed stance on continuity, I personally would have no problem seeing material from the Rise of the Empire era alongside Rebellion era content in the same Force Pack, so long as each followed a consistent theme (in a given cycle, there could be a "Jedi Purge" pack followed by a "Declaration of Rebellion" pack, for example).
But none of this ought to be necessary right away. After all, the Classic era is where the money is, and without even deviating from the main saga aside from following the existing trend of slipping in subtle nods to the Expanded Universe, there is easily enough material to cover four more cycles of Force Packs after Hoth, by which time Episode VII will have made it into theaters. If FFG indeed has plans and permission to expand the game beyond the Classic era, the next place it is likely to go with the license is the new film.
So let's just hope it doesn't suck.