IMO better gameplay + replayability is always more important than being realistic. Think of the best games you have played. They do not have to be totally realistic to be fun. Skyrim: Shooting fireball out of your palm; Max Payne: slow-mo bullet time; GTA: hijack any car within 5 seconds. Oh and Saint Row, the fun of this game is the unrealistic parts. Even realistic game like ARMA 3 has parts that doesn't make sense if you really think. The same is true in Xenonauts.
I don't mean Xenonauts should be like Saint Row. But adding more game content is always better if that's feasible. We can always think of something that make sense and suit well into the story. Here are some suggestions, some of them are inspired by you guys:
Locating and rescuing MIA soldiers/pilot: Triggered after your intercepter got shot down. Within 24 hours you have to land a rescue team to search for your pilot and bring him to your dropship. The pilot is "activated" when the other xenonauts members arrived. He has a pistol on him and he only has half hp and TU.
Escorting VIP: whoever is the VIP doesn't really matter. Can be your hired scientists that get cornered by a squad of alien scout. Or a rich businessman who is funding the xenomauts project. Or the president of the region that you are about to lose. Escorting him/her to your dropship with aliens attacking from all directions. The outcome will be improving the relation of that region/ gain free scientists, funding, etc.
Military base defense: not the xenonauts base. Survive a number of waves of alien attacks with at least 1 local force surviving. Get a couple of new recruits to the xenonauts team.