Change Gamepad Buttons At Driver Level?

I recently installed Matrix: The Path of Neo, which is a great game, but its PC port is horrible.The problem is, the game detects any gamepad and maps its buttons automatically, with no options to change the buttons.So, the game uses the right analog stick to manipulate the camera but the X and the Y axis are switched so, what I wanted to do was to make Windows 'think' that the X axis is the Y axis and vice-versa.I already searched the internet and couldn't find any program that did this (xpadder, pinnacle game profiler, motionjoy, joytokey, none work)