Are you sure you could only fit in one? My heart says Fantasmic as its amazing but my head says More bang for your buck, do Wishes and Spectromagic. I think most folks would agree that for kids, Illuminations is the one to miss.
If its just a case of the late finish, your kids may surprise you. The year we took my DNephs, the younger one was 3. At midnight hes still riding the Dumbos! At 12.30, back in the hotel room, hes watching a movie on the Disney channel. My DS and DBIL fell asleep and left him to it. If you know its going to be late night, you can always schedule a siesta and a late morning next day. Whatever you decide I know your children will love it-have a great time.