Id be happy to see the missions give bonuses to their associated skirmish map. This is something realistic and i think muse should put some emphasis on skirmish / alliance interplay.
that.
Another thing popping up in my head:
I also imagine some sort of gamemode where you play Alliance against each other (2v2 maybe) but can't fight directly. More like your skill and performance in certain tasks and missions determines how many AIenemies (like a sort of minion) spawn that will try to prevent the other team from completing their tasks.
I don't know whether and how this could be realized in a balanced way without "endless combos" (fail once and there is no chance for comeback), the possibility to see how and what the opposing team is doing, but not being able to interact (if ramming is forbidden there must be physical separation, but that hinders visual feedback. or ramming could be allowed. AI enemies maybe will need teamcolors) .....
I only have a very vague idea and I guess it would be complicated to make and maybe to play, but I also think that it could be fun ^^