On Linux, joysticks should by default be sorted by their device files (/dev/input/js*).
Joystick 1 should be "/dev/input/js0", joystick 2 should be "/dev/input/js1", and so on. This was the default behavior on SDL 1.2, and it simply worked.
Currently they are sorted in the opposite order. Last joystick always gets enumerated as "joystick 1", the last but one always gets enumerated as "joystick 2". This is super counterintuitive.