I just wanted to report that I am having problems using the gamepad with the Fire TV in a C2 game. When I tried Cocoonjs, no gamepad input was registered. However when I tried Intel XDK Crosswalk, it registered a few button presses for awhile but later builds didn't register anything. It's possible the gamepad inputs were also mapping keyboard keys since I had both Gamepad and Keyboard events, I don't know.
This is different than justifun's experience. He said he was able to map an Ouya game controller to the Fire TV in a C2 game.
I'm hoping someone will look into this eventually and if there is a problem, create a controller plugin.
Controller I'm using with Fire TV: Moga Pro Power (works with everything else Fire TV perfectly)