First off, I really like the ability to use non-Xbox gamepads in the new patch. However, gamepad mapping doesn't seem to work on Linux. Clicking on controller select for each character causes a crash. I got around this by editing the settings .xml to manually set each player's gamepad (default was to set all to 0). I had another crash attempting to bind a key with an emulated xbox gamepad (via xboxdrv), but that setup is no longer necessary with the switch to SDL2, so this probably doesn't matter. Additionally, with the "Detect as Xbox gamepad" option checked, there is a constant left input seen (this is with two standard X360 gamepads and a Logitech F310 in Xinput mode). These controllers still work fine without the option checked, though. Finally, when I did fix the controller settings, the controller toggle on the settings menu began to work, but only once -- I could toggle controller0 to controller1, but a further click caused a crash.
Hope this information is helpful. I tried to read the crash logs but they seemed to reference mono in some way -- I'm guessing that isn't useful.