I just finished my Retropie, pi2, and RP2b2.
I first tried option 3 of the xbox controller setup, but, although jstest correctly identified my controller, no button pushes registered. So, I renamed the xboxdrv files, and tried option 1, which worked perfectly. Just a data point.
I did find that for Mario Kart, I had to remap via the AutoInitcfg.ini, the “Z” button trigger (which I mapped to the RT), and also the start button. In mupen64plus.cfg, I mapped the “exit emulator” to “JOB10”, which is the big “X” button in the center of the xbox 360 controller.
Mario Kart now works fine, and I can exit no problem.
For the record, I have experimented with SNES-type controllers, N64 (Retrolink) controllers, and Logitech F310 controllers along with MS xbox360 wireless controllers. The xbox 360 wireless controllers are (by far) the most elegant solution. The Retrolink controllers are horrible. The SNES controllers are good for little kids, and work well with Sega, Atari 7800, NES and SNES games.