You can hardly blame SDL for this, games are not really what X11 was designed for. Setting up full screen and asking for exclusive access to the keyboard will prevent the window manager from doing anything to it.
My solution for this problem: use a window manager that can full screen any window and switch back.
> and the joystick will still not be recognized if you plug it in after the game starts.
To be fair, 99% of AAA games don't support joystick hotplugging either. It's really annoying.
Since you have not checked whether this is actually the situation and do not properly understand the other components in the equation, I find your attitude offensive.