Currently, it's quite awkward to play the game with a controller, not counting the menus. (Which only half work, anyway.)
What I'm mostly talking about the item belt (pills, vials, barriers, etc.) and sprite actions. They are currently aligned in a row, perfect for using the number keys...but it's not so easy when you, say, assign them to a D-pad. Then you have to remember what is where on the pad and it's easy to make mistakes.
So what I suggest for this controller mode is that the item belt and/or the sprite actions would be arranged on in a plus-shape. It would either go under the game tab or the controls tab within the ESC menu. There would probably be a check box for both sets of actions, so that players who map their belt to the D-pad and then the sprites to other things wouldn't have to have a plus-shaped set of sprite actions. (Personally, I would put the Sprite actions on the D-pad, and then the items would go to Modifier+D-pad.)
Also, an option to modify/customize the UI entirely would be lovely.