I'm having the same issue, have all the drivers installed and tested in the usb controller settings to see if my controller is responsive. Plays flawlessly on other games with controller support, and is detected by dolphin, but the inputs stay grayed out. I do have xinput/0/gamepad selected, so that's not the issue. I live in Japan and the layout is in Japanese, but other than the language i find that all the settings are in the same place and do the same thing on the English version as well.
Screenshot: http://imgur.com/a/c4aKS
Screenshot: http://imgur.com/a/c4aKS