maybe something like fetch a big bomb into an alien infested bunker- youd just need to bring it on the lowest level and (optionally) get out in lets say 20 turns- if you dont you loose anyone who was left in the building.
Of course it would need a reasonable mapmaker who will not make a labyrinth with only one way resulting in need of killing all aliens on the map
COOL!
In fact, I would say that the "Shelter" map would be a good option - many ways in and out. Flood it with 3-4 times the number of aliens , specify the drop location deep in some lower level...
I bet it would be fun to sent two teams, one to make a lot of noise (explode grenades, launch rockets) to draw attention of the "hosts", while another group with rifles and SMGs (relatively) quitely makes its way down to the basement. In the mean time, the "noisemakers" pretend to be bogged down, and in reality are protecting the retreat of the real incursion team.
A similar mission can work for a huge alien ship - too big to be taken down by anything humans have, so the only option is to fight our way in and place a small, man-portable nuke on board. Can make in-game nukes, too: large backpack item, very heavy. Effectively, a strong soldier can carry that and an SMG maybe.
Suppose could be carried as a last-ditch option on any mission - loose everyone who has not left, kill 100% of aliens and civilians guaranteed, the local nation becomes VERY not happy.