In original X-com i didn't liked, that killing aliens was more profitable than taking them alive and the only gain was a piece of information about their species/spaceships/other species after interrogating the first captive. After discovering martial solution any other leaders or commanders was useless. So why don't we get some random intel about aliens operations, after succesfully taking prisoner high ranked alien?
For example after capturing and interrogating common soldier from light scout we can learn about his goals(his mission, target etc.), when we force alien officer to "confession" we can learn about location of alien base, planned attack on city X in the nearest future or for very short period of time we can see movement of aliens craft without need of radars. Of course it will require some way of communication with aliens, like learning their language, but it could be done with 2-3 researches.
I think it will be interesting way to fight alien invasion.