5. Multiple choice quest branches. Like maybe in that one mission where the Klingons claim the Vulcan Ambassador is an Undine spy, you would have the option of scanning the Ambassador. Maybe tie it in with option 4 and then have to chase the Undine across your ship.
That would have been a good idea for that episode. I felt guilty after I had fought/ killed all those Klingons just to find out they were right.