Configuring Input settings by hand is very annoying and not very flexible. It is stored as a project settings so reuse is poor. It is a nightmare to setup custom controls for multiple joysticks (XBox supports up to 4 gamepads). I'd like to have my own XML config which I can load at runtime to setup controls and share it between my projects.
So I suggest UNITY developers to add the ability to configure the input programmaticaly.
Please vote for this topic if you think this is important for you. I hope this will make some noise.