That's kind of the same problem I have when switching from one style of game to say an RPG, only usually when it comes to RPGs I'm more used to Circle being "confirm" and X "cancel" mainly due Final Fantasy and Japanese imports where Circle is generally confirm an action for most games.
Actually while on the subject and that last bit it reminds me of the US version of Devil May Cry. I decided to purchase it after owning and playing the Japanese version to death, and DMC3 was on the horizon, only to find to my horror that the controls were mapped completely different the Japanese version that couldn't be changed and essentially making it unplayable which is why to this day I've never finished the NA version.
Right now I'm having to adjust and get used to the controls of another game because I've switched from a beat 'em up called
Yakuza to
GUN which is an action title that utilised the second analog stick to aim when for Yakuza I didn't need to use it once.
Jam it back in, in the dark.
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Simo