A huge departure from the original, but what if there were other missions, and maybe non main storyline missions. Like something out of the original laser squad or rebelstar... They had missions like get to the other side of the valley with the device, or steal device, or get into the control room....
I don't know, rather than exterminate aliens maybe there are other things we can do, like more detailed alien bases, capture commander.. well, that exists though for some reason I always get away with very large ufo commanders....
How about assault the farm house? Destroy the comms station with high explosive?