This fix is SPECIFICALLY for Xbox 360 controllers, although I assume that in the file mentioned below, you can edit other kinds of controller by finding the specific controller ID. This fix also sets the Xbox 360 controller and setup as the defaults.
1)Navigate to the C: drive of your FIFA bottle by, in the Manage Bottles menu, going to Advanced, then click 'Show C Drive in Finder'
2) Find the file buttonData.ini or buttonDataSetup.ini- it should be in somewhere like 'Program Files/EA Sports/ FIFA 12/Game'- and make a backup of it elsewhere (Just in case something goes wrong)
3)Open this file in TextEdit or a similar basic text editing program
4)Find the section which begins: AddController "Controller_45"
(Search for AddController "Controller_45" to take you directly there.)
5) Replace the section below this (but above the next 'AddController "Controller_X' section) with:
(Just copy and paste ONLY the WHOLE section with grey shading, INCLUDING the indents at the start of each line)
AddAlias "Default"
AddAlias "Default Pad"
AddMap PC_AXIS_0_DOWN VB_AI_LS_DOWN
AddMap PC_AXIS_0_DOWN VB_FE_LS_DOWN
AddMap PC_AXIS_0_LEFT VB_AI_LS_LEFT
AddMap PC_AXIS_0_LEFT VB_FE_LS_LEFT
AddMap PC_AXIS_0_RIGHT VB_AI_LS_RIGHT
AddMap PC_AXIS_0_RIGHT VB_FE_LS_RIGHT
AddMap PC_AXIS_0_UP VB_AI_LS_UP
AddMap PC_AXIS_0_UP VB_FE_LS_UP
AddMap PC_CONTROL_BUTTON01 VB_AI_A
AddMap PC_CONTROL_BUTTON01 VB_FE_SELECT
AddMap PC_CONTROL_BUTTON02 VB_AI_B
AddMap PC_CONTROL_BUTTON02 VB_FE_CANCEL
AddMap PC_CONTROL_BUTTON03 VB_AI_X
AddMap PC_CONTROL_BUTTON03 VB_FE_X
AddMap PC_CONTROL_BUTTON04 VB_AI_Y
AddMap PC_CONTROL_BUTTON04 VB_FE_Y
AddMap PC_CONTROL_BUTTON09 VB_AI_START
AddMap PC_CONTROL_BUTTON09 VB_FE_START
AddMap PC_CONTROL_BUTTON10 VB_AI_BACK
AddMap PC_CONTROL_BUTTON10 VB_FE_HELP
AddMap PC_CONTROL_BUTTON13 VB_AI_LDPAD_DOWN
AddMap PC_CONTROL_BUTTON13 VB_FE_LDPAD_DOWN
AddMap PC_CONTROL_BUTTON12 VB_AI_LDPAD_UP
AddMap PC_CONTROL_BUTTON12 VB_FE_LDPAD_UP
AddMap PC_CONTROL_BUTTON14 VB_AI_LDPAD_LEFT
AddMap PC_CONTROL_BUTTON14 VB_FE_LDPAD_LEFT
AddMap PC_CONTROL_BUTTON15 VB_AI_LDPAD_RIGHT
AddMap PC_CONTROL_BUTTON15 VB_FE_LDPAD_RIGHT
AddMap PC_AXIS_1_UP VB_AI_RS_DOWN # Right Analog Down
AddMap PC_AXIS_1_UP VB_FE_RS_DOWN # Left Analog Down
AddMap PC_AXIS_1_LEFT VB_AI_RS_LEFT # Right Analog Left
AddMap PC_AXIS_1_LEFT VB_FE_RS_LEFT # Left Analog Left
AddMap PC_AXIS_1_RIGHT VB_AI_RS_RIGHT # Right Analog Right
AddMap PC_AXIS_1_RIGHT VB_FE_RS_RIGHT # Left Analog Right
AddMap PC_AXIS_1_DOWN VB_AI_RS_UP # Right Analog Up
AddMap PC_AXIS_1_DOWN VB_FE_RS_UP # Left Analog Up
AddMap PC_CONTROL_BUTTON05 VB_AI_LB
AddMap PC_CONTROL_BUTTON05 VB_FE_LB
AddMap PC_CONTROL_BUTTON06 VB_AI_RB
AddMap PC_CONTROL_BUTTON06 VB_FE_RB
AddMap PC_AXIS_2_RIGHT VB_AI_LT
AddMap PC_AXIS_2_RIGHT VB_FE_LT
AddMap PC_AXIS_2_DOWN VB_AI_RT
AddMap PC_AXIS_2_DOWN VB_FE_RT
NB: Do NOT replace any other part of the file!
4) Save the file.
Now the Xbox 360 controller should work- I've tested it with an official wired version and it works.
Alex