Suggestions coming from a PC player, feel free to disregard if this isn't the main targeting platform.
[Difficulty selection]
1) Allow starting game by hitting confirmation button on the gamepad.
[Options menu]
2) Improve visibility of currently selected buttons
[Options -> Controls menu]
3) Currently it is not possible to change bindings using gamepad.
4) Consider changing icon for “A” button, this took me longer to figure out that it should have.
[Other]
5) Add option to limit FPS and/or VSync.
*) Allow player to pause the game.
6) Consider switching whole UI layout in widescreen mode.
Attaching pictures to illustrate better.