One of the problems -- outside of the obvious -- with a significantly damaged aircraft is that pilots often overreact and add to the situation. In other words, when a plane gets nailed by something like a missile, the person at the wheel panics.
DARPA and Athena's Damage Tolerance and Autonomous Landing Solution adds a full flight automation and backup system that uses a plane's internal inertial navigation system and GPS systems to land safely by automatically adjusting to the new configuration -- a physics computation that a human is in no condition to deal with during such a crisis. In a recent unmanned flight test, Rockwell Collins showed off the tech with a scaled-model F-18 in which nearly half a wing is blown off and then landing the plane safely. Check out the video:
http://www.rockwellcollins.com/news/video/damage-tolerance.html