Another good topic. This is the kind of stuff that's actually useful to me as GM, unlike the endless debates about a Disney cartoon I'll never even watch. Let's stick to the game , huh?
I think EoE would segue pretty seamlessly into a rebel game, but I'#m keeping mine separate. The characters might bump into each other though. The EoE group lacked a PC with Pilot/Planetary, so I let one player use his new AoR character, who is a hotshot racer, when we ran the Corellian speedbike scenario.
I also plan to have the leader of our AoR team to hire the EoE team to kidnap her possibly-Force-sensitive daughter from the Alliance before she gets enrolled in Project Emergent...
Project Emergent?
And yeah, things seem to be pretty seamless so far. I'm tempted to keep the games separate, but given my epic level visions for EotE, it'd be hard to ignore a rulebook tailored toward that massive, era-focusing war.