One of the biggest limitations I've run into with the ardupilot hardware is the use of functions that need to disable the interrupt register to do precise timing such as pulsein() or similar functions. Would the 1280 have the same issues?
Have you guys considered a dual processor design for the Ardupilot? I can image I2C connected chips would give you the ability to offload the radio input and give you multiple UARTS.
Are there any other design considerations for the next generation board or for an alternate design?