It'd be nice to see them cut back or give you the option to turn them off. I understand that they're supposed to play a major role in the game but they have a tendency to show up either at the worst of times or they'll show up and do everything for you.
I've noticed to that when you take out a boss there seems to be more of them in the area. Maybe it's just me but I'd hate to see rebels do what they did to Far Cry games where it slowly widdles away at the game because they start pushing out enemies until they're only in one area.
Other than that my friends and I have really enjoyed the game so far.