i never even thought about using an xbox 360 controller.
i think with the joysticks it would make flying around and dogfighting easier, but with as many controls as EM has i dont know it would be great for every situation.
if i get fed up with the keyboard and mouse i'll try it out.
Try out my xpadder profile. All of the ships main controls are mapped to the buttons (movement, shield control etc.), but when you push 'LB' you also get secondary and mouse controls. It actually works very well and I would use it if I didn't have my x52 pro - actually I made this profile for legends so I could play on my netbook.
I re-uploaded it, the link above is new and working.
Click the grey 'download this file' button then enter the code.
edit: Just checked and I actually do have a mercenaries profile, it's the same as the above except for vertical strafing. I would still download the top link though because there is a diagram with instructions included.
What did you unzip it with? I used winrar to pack the file so using it to extract might help if you haven't already.
Could be that the profile was made for an older version of xpadder though i'd expect it to be compatable. Have you also copied the controller cofiguration file over?