I did some more testing, and this is what I gather.
When using pad controls, autoaim seems to work when moving even if the autoaim checkbox is unchecked. Right stick aiming only works partially, it seems that I can only shoot to three directions, up, down and back. Shooting wherever Maija is facing doesn't work, and neither does none of the in-between directions.
edit:
As someone said in another thread, the broken right stick aiming was because the 's2ax' is by 4 default, and can not be changed within the game. I edited the xml file and changed it to 2, the right stick aim works now, in all directions.
The whole autoaim business still remains though.