I never got used to playing Rebels vs Rebels or Empire vs Empire, for me it just looks wrong, same side fighting with each other. If I have to play it I would do it but I don't enjoy it as much.
For tournaments I wish each player came with one Empire and one Rebel fleet and as they progressed further at each step they will switch fleets from E to R or visa versa.
Normally I would be afraid to suggest this as it is quite expensive to have both fleets. However I just read a recent thread where players discussed their fleet size and oh boy, a lot of people had crazy fleet sizes. I know, people with a lot of ships contributed to that thread but still, serious players really do invest at all factions.
So maybe at bigger tournaments this could be applied or is it just me that is bothered with this?