One thing that might be nice, if it is implementable, would be to include pilot characters. That is, in the original X-Com there were soldiers with stats, but pilots apparently were bought and sold with their craft. It might be nice to have pilots with their own stats that would effect how alien craft are shot down. Perhaps one pilot has a lot of skill in maneuvering and so he is able to stay on the UFO's tail (or even gain), whereas another pilot might have good dog fighting capabilities, which would ensure a greater chance of shooting down the craft, while yet a third might have good targeting capabilities so that the craft is shot down in better condition.
As for the actual event itself, I would recommend something simplistic for the player. One can't really turn air combat (are all "UFO" flying? do some swim, or dig, or walk, etc?) into strategic combat. Perhaps "combat" like in the old rebel assault games, where the player doesn't really fly the craft, but just aims the weapons?
Just a,
Thought