There have been a few threads about similar things already and I personally am not too keen of prequel factions, but I found a way to implement them that wouldn't bother me as much. It struck me that the Rebellion actually doesn't need a new subfaction for the whole thing to work, just as Scum didn't get one with the new TFA stuff. That would make the CIS part of Scum and the Republic part of the Empire. There are still some issues with that, like Jedi flying for the Empire (which could be solved by just not printing Jedi pilots, but i guess that wouldn't be too popular), but it works better than other ideas.
I don't think FFG will do prequel stuff any time soon or even at all, but I guess if they do, there is a way that won't be total nonsense.
