I feel many more different missions could be created by:
1) switching side you are on in the mission, for example instead of helping gov protect police precinct, you help Mutant alliance/smugglers/rebels to break out their buddies out of police precinct; assaulting government base instead of defending it from Ninjas (maybe with humanists defending the base instead of gov) and so on
2) same mission, different environment, mostly doing hunt/primal hunt missions in tunnel maps (megascorpion layer and what not). these would naturally more challenging, as melee animal AI is so weak in open area maps, (just milling around while you shoot poor beasties to bits). in some missions, these cave layers might have static "nest" enemy unit that continually spawns beasts and must be destroyed with flamers/explosives, similar to zombie portals in missions with pyramids.
Making these missions shouldn't take devs much time i imagine, as all the assets used already exists in game, and would add a metric ton of new experience for players to enjoy.