The problem is that all the WC games automatically assign Button 1 and Button 2 to two of the face buttons. The above applications only let you map keyboard keys and mouse buttons to your controller, they don't let you remap controller buttons to other controller buttons. It's particularly bad for Prophecy, which will also assign Look Forward / Look Left / Look Right / Look Backwards to four more buttons, leaving you with 6 buttons you can't reassign. Xpadder et al. help a little, but it'd be pretty hard to make a really comfortable config, especially if you use both sticks.
Some controller manufacturers make available programs that do allow remapping their controller buttons natively. I guess the 360 controller doesn't have anything like that. Unfortunately, the only advice I can think of is to buy a controller that does.