Glum,
"Ultimately there may not even be a joystick... "
I've got in trouble before now for pointing out that most current transports can be flown without manual control input from around 500 feet after takeoff (Minimum Engage Height) to touchdown.
Please post a link to your team's project when you've finished it - as Genghis has said, it will be interesting - and refreshing - to see what could be done especially when you don't have to consider the impact of legacy systems or traditions.