I found instructions for how to do this with Saints Row The Third, but had no success with them. I had the controls set up, not just as I'd like them, but usable, and suddenly the game decided that D-Pad up would give me the map, instead of calling homies as I had it set to do. I checked the settings and they are as I left them, but the game just wants to do things its own way it would seem. I'd like to just bypass the game's gamepad support and make an Xpadder/Antimicro profile which would give me complete control of the mapping instead of the badly ported and inflexible gamepad support built into the game. These kinds of issues are so common with games that I actually get really excited when a game has NO gamepad support, because I can just remap the keyboard and mouse controls and have no issues such as these.

I found a solution to disable the xbox gamepad recognition in both Saints Row 2 and Saints Row the Third in order to use Xpadder to set the controls up exactly as I want them and thought I'd share the info. I used TocaEdit Xbox 360 Controller Emulator. Drop the (32-bit, for these games) application in the game's directory and run it. It will want to create a dll and an ini file, allow it to do so, then set all the controller buttons to empty (no assignment) by hitting clear. Save the changes and close the app. You should be able to just copy the dll and ini files to another game's directory and not have to run the app again. Now you can set up the controls however you wish with Xpadder or similar.