If you have the Steam version of the game and you can't get the game to register your controller, could you try this out?
1. Disable the "Steam Overlay while in-game" option in General tab(it doesn't even work anyway, as far as I'm aware).
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2. Select the "Enable Steam Input" option in the Controller tab.
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3. Go to controller layouts and select/customize your layout(I used the default Gamepad one but swapped the X and A buttons).
4. Launch the game via Steam.
And hopefully it'll work? I got this game in... December? and I couldn't get my PS4 controller to register no matter what the hell I tried, I turned off the Steam Overlay option on a whim and now the controller layouts work flawlessly plus I can use the whole controller instead of just the left stick/X/O buttons.