Hours and hours of my early gaming life was spent playing Wing Commander, X-Wing, Tie-Fighter, and Stunt Island. (One of my earliest memories was playing the original Falcon on my XT.) In those games, the Y-axis -- the up/down axis -- was always inverted. Pull down on the joystick and the nose of the craft would incline; push the stick forward and the craft would angle downward.
The control method ingrained itself so deep into my brain that when consoles began to come packed with controllers that featured dual thumb sticks -- and even before that with the N64 controller -- I played with the Y-axis inverted. (Playing with mouse and keyboard, this issue just goes away.)
Gears of War, TimeSplitters, Prototype 2, Halo, LA Noire, Batman: Arkham City, Rainbow Six Vegas, Stranglehold, Max Payne, the list goes on... games and series that I've played inverted. It helps to cement that Y-axis quirk that was established so long ago. So, when I come across a game, especially a modern game, that doesn't feature the option to make that switch (or even makes it the default control preference) it's enough to completely stonewall any enjoyment I might otherwise squeeze out of the game.
Right now I'm thinking specifically of Ghost Recon: Future Soldier. The PC version of the game.
