I suggest some ufos to be treated by the army without serious player interaction in the late game.
I mean when you are fighting battleships you don't need to shot down and capture small scouts. Seing military airforces flying around would add a lot of flavour and remove the headache of boring supereasy battles. But if you let army to treat some ufo and they would take serious casualties you would recieve a penalty.
This idea was in the Vladimir Vasilyev's Enemy Unknown sci-fi book