With all the neat customizing and player-created scenarios out there, has anyone tried playing mixing rebel and imperial ships on a side?

What rules might need adjusting to account for that?

 I haven't gotten to the point yet where I would mix factions to spice up the game, but there's no reason why you couldn't do it with your group.  Just make sure you use the number tokens and the two coloured sides to ensure you don't get the owners mixed up.  It would never fly in official tournament play, but among your group, I always say that if it makes the game more fun, go for it.

 I don't play with a gaming group…just me and my kids so far. But I can imagine that it would be fun for us to play with mixed team play.

Can you think of any rules that would not work with this scenario?

Initiative might have to be determined with a coinflip, but nothing else stand out on first thought.

Not allowing duplicate unique characters or items might be a good thing too.

 Honestly, just go for it.  Even in a tournament, if I brought Imperials, and so did my opponent, there's a good chance we'll both have Darth Vader out on the table, which is totally allowed for in the tournament document, so Unique Pilot mirror matches are technically "official".

The only rule you're "breaking" is mixing the factions.  Just play it a few times and let us know how it goes.  It's hard to troubleshoot any potential rules corrections until there's some data from actual gameplay to see what's good…or not good.