I've often wondered if maybe sitting upright might not be the best position for a modern combat pilot. I can see pilot who is laying down pulling far more Gs than even a legless one sitting upright.
The other thought about legless pilots is the feet I think are used for the rudder control (pedals), so there is some loss of ability to control without using your feet. While I think computers could probably take this over, in the end it does mean two less things to interact with the plane.