IMO it is about the flight characteristic of the UAV and not the flight control boards/software you are using. The telemetry component may have some impact on the boards.
I have used both paparazzi and APM. I think APM is more user friendly because it can run on Windows but you need to have UBUNTU/LINUX to run paparazzi. You need to know a lot about C++ to use paparazzi.
PS I am not an expert so somebody can give you more/different opinion.