The controls are a nightmare to setup properly on this game compared to MGS1 and for whatever reason the right stick doesn't seem to register on my controller while on the controller setup screen on the MGS2 launcher... well it kinda does as clicking it registers but moving it up, down, left & right does not work at all. As far as I know the only way to be able to play this game properly with a controller is to get the MGS2 V Fix but I think they should definitely do some sort of patch or something for this game to make the controller work properly out of the box because at the moment it's really awful tbh and it probably turns a lot of people away from the game. Oh and I know the MGS2 V Fix is the best way to play this game but at the moment it seems to break some features with the GOG version like cloud saves and the direct x settings so I will probably just wait until they are addressed at some point before I install that fix.

No problems setting controls in GOG version for me. V Fix was nice for CD version, but it disables dInput controller setup.

Is that so?. It's so strange because my controller is a DS4 which is a DInput controller but for some reason I just can't get the controls to work properly on my end... what controller are you using if you don't mind me asking...

SVEN X-PAD. I also used Genius MaxFire G8 and two DVTech controllers in the past. All four works perfectly with MGS2. I didn't try my 360 and XBOne controllers though since X-PAD works great as is already.