Some house rules I'm considering. Before please note that as the Imperial player, I run the game a little bit more like a GM (which my group and I enjoy) such that everyone has a good time. I like it to be thematic (Will play snowtroopers only if there are snow tiles, will keep Winged guards in Bespin setups, etc.)
1) If they wish to, let the Rebels "hire" a bounty hunter for a given mission in replacement of bringing an ally. That would be thematic in missions where you have to defeat a villain, i.e. final mission of a campaign. To "hire" the bounty hunter, they would have to pay credits (no threat cost). Basically, they would save credits earned and pay something like threat times 100 (still on the design table) to "hire" the bounty hunter. For example, to use Bossk as an ally, the Rebels would have to pay 800 credits. Of course, the draw back is that they commit money that could have served to upgrade equipment, but if the bounty hunter is brought in on the final mission that might actually be an advantage given the extra activation.
2) For some creatures, like Wampas and Nexu I assume these are wild beast that unless specified by mission scenario shouldn't have any specific allegiance toward either Imperial or Rebel camps. With their supposedly limited intelligence, they should go after anybody, no matter if rebel or imperial. So what I plan to do when such a creature is on the board is to activate it first every round. Roll a green die, if a surge shows up, that creature is controlled by the Rebels (for that round) and they may use it as a temporary ally. If no surge shows up, then it's the Imperial that gains the right to activate the creature. Re-roll the green die at the start of each round to see who controls the creature.
Again keep in mind that I am leaning toward a more thematic game experience rather than the competitive atmosphere of the out-of-the-box campaign rules. I'm 100% aware these house rules are not suited for everyone.