My ideas for this design center around the need for a stable aircraft, either via its own inherent stability and/or provided by an on-board IMU or AHRS. In my case I'm relying on an ArduIMU for stabilization. Once I get the time I'd like to study further the possibility of using one 3 axis accelerometer for short-term pitch and roll stabilization for inherently stable airframes. I'm flying foam aircraft, up to 24 oz in weight and really low wing loadings so this design concept is not a one-size-fits all out-of-box. Right now my airborne code is very simple. The ArduIMU takes over as soon as all channel changes stop. So it is a crude fly-by-wire setup. The ArduIMU roll also limits the roll of aircraft to 60 degrees even under manual control.
I haven't gotten into the PID, turn-rates, navigation, and other heavy computing and will definitely be studying the ArduPilot code for guidance.
I want to give a big 'thank you' to all those responsible for developing and sharing ArduPilot, especially Chris and Jordi, you are an inspiration to us all.