Or, as a hack, you could directly change the mapping inside the python generator script:
Edit:
/usr/lib/python2.7/site-packages/configgen/generators/dolphin/dolphinControllers.py
And, for example, change line 21 from:
'x': 'Buttons/2', 'b': 'Buttons/A',
to:
'x': 'Buttons/A', 'b': 'Buttons/2',
Now the WiimoteNew.ini file under share/system/configs/dolphin-emu/ will be always generated like you want (until, maybe, the next system upgrade or something).
This is the end code (just for reference):
def generateControllerConfig_emulatedwiimotes(playersControllers, rom):
wiiMapping = {
'x': 'Buttons/A', 'b': 'Buttons/2',
'y': 'Buttons/1', 'a': 'Buttons/B',
'pageup': 'Buttons/-', 'pagedown': 'Buttons/+',
'select': 'Buttons/Home',
'up': 'D-Pad/Up', 'down': 'D-Pad/Down', 'left': 'D-Pad/Left', 'right': 'D-Pad/Right',
'joystick1up': 'IR/Up', 'joystick1left': 'IR/Left',
'joystick2up': 'Tilt/Forward', 'joystick2left': 'Tilt/Left'
}
