We've certainly reached a point in the game where players who own at least one of each expansion and blister have a huge amount of variety. Also, it seems unlikely that, as cool as HotE is, that it'll be many new players' choice for their first expansion.
With those things in mind, I wonder if we're going to see the HotE story missions have a much more strict limitation on mixing Mercs in with Imperials. We've already seen this with some missions in previous boxed sets- but from the description of the conflict in HotE, I can almost see Merc and Imperial troops on Coruscant not working together at all.
In fact, given the sort of standoff between the three factions, it might be an interesting idea to offer mission-specific allies in the form of Merc and Imperial units (I know that certain expansions have done stuff like this before). It'd be neat to see the Rebel heroes working alongside a Royal Guard Champion to take down IG-88, or to have the Rebels team up with Maul to try to survive Vader's onslaught.
Just a thought. I'm sure having less flexibility in open groups would frustrate some Imperial players, but I think it fits the flavor of the campaign really well. Plus, it's not like this is some new mechanic- it would just be an expansion on an already existing one.