Wow, I very much enjoyed this. I’m impressed. Well polished, too.
I would agree that having a fullscreen option would add to this game. Perhaps it could simply be off by default, but be enabled via an option in the options menu. I think that on Linux you shouldn’t have trouble switching to fullscreen especially if you set the window size to base.pipe.getDisplayWidth()/Height() so that no resolution-switching is needed; do file an issue report if you experience otherwise!
I tried plugging in an (Xbox One) gamepad at the main menu, but it caused the cursor to switch erratically between the options; I suspect that this is because the Xbox gamepads don’t properly report a value of 0 when they are centered. I would suggest that for directional controls like in menus you build in a considerable deadzone, so that eg. only inputs of 0.3 or greater will trigger a switch to the next menu item.