All stories get tiresome if they get repeated over and over. Not the best of points if you ask me.
What I'm saying is that while the generally self-serving members of an EE campaign can be 'tbought' by the Alliance for an AR-themed adventure (like Han Solo was), the opposite is less true. A fighter pilot/commando/commodore isn't likely to be able to constantly take time away from their duties to the Rebellion in order to go help out the Trader and Scoundrel with their newest scheme. Sure, it can happen once in a while, but 'odd couples' like this don't make for good permanently mixed groups in my opinion unless the EE characters are pretty much willing to give up their independence (like Han Solo and Lando who both pretty much sold out to the Alliance/New Republic and became AR characters that just happened to start with EE careers).
You've never been in the military I take it? A completely plausible story for the AoR is they just got plain sick of war and chains of command and walked away from it. Lots of us have.

