Option 3 for me, in that these are new factions that cannot be played with or against existing factions. Sorry, I don't like Option 2 at all, and the idea of CIS vs Empire or Republic vs Rebels bugs me in the same way that a game featuring a battle between WW2 Japanese and WW1 Germans would. My feelings are the same with the ST era.
All the same rules. Just new core sets. Non-unique upgrade cards can be used in any of the eras but otherwise start releasing ships and characters from scratch (obviously you can reuse and repaint a few of the models).