In 2.6 it appears Input is read-only and can only be defined in the Inspector or at the start of the game. We would like to provide our own settings view that could set these values via scripting. I've seen some 3rd party solutions to this but I am wondering if it will be available as part of Unity 3.0. If so, we'll hold off until then.
No, there won't be any major changes to the Input Manager in 3.0.