That is true, with a mounted weapon you do lower the rear of the weapon since it is mounted on a centered pivot, which is why I clarified that I was talking about a rifle and pistol. These are the two most common types of weapons used in shooters and similar games. In comparison, mounted weapons are rare and in most multiplayer games, hardly used since they are basically sniper-bait.

After Burner, Air Diver, Top Gun, Ace Combat, Wing Commander, Colony Wars, & Decent: Free Space are some of my most favorite games of all time... just wish we could get some space shooter love for Gen7.

Hopefully more devs will see what Bungie is doing with the space combat in Reach, and will get their acts together.

No it actually makes sense. Just think about it this way:
If the weapon is a rifle to aim upwards your head and your gun is tilted towards you. Same goes with a handgun. As you aim up your weapon points in the same direction as you look at it with an inverted arrangement of the stick. Inverting the X-axis on the other hand doesn't make sense imo because you don't use the X-axis to tilt your gun but to turn where it is more logical to think. Right = turn right etc.
Edit: That is assuming the controller is horizontal.
@Bellow: Exactly, that's what i meant. Also applies if ou imagine the stick is the upper part of your body.

Yeah, you don't pivot the rifle by dropping the rear, you're actually pulling it up, but the movement is still a clockwise pull down, just like you would do with the analog stick.

Ok video game nerds and non real life gun owners. How you you hold a controller? I hole mine level so the sticks are pointing up so to me I push forward on the stick to point down and pull back to point up. When you hold a real gun like some of us that actually have guns, you pivot your wrist and body forward to point down and vice versa to point up.

If you're on top of a building and you want to point down to shoot something which way does your body pivot/move? Just imagine your body as the stick. But like I said before I hold my controller level with the sticks points up not sure about the rest of everyone out there. Inverted Y-axis feels more like a natural body movement to me.

My reasoning for inverted or not is based how the object pivots in the game as others have said. When playing a game with a gun I view that as pointing a cursor at something. It makes sense that up would move the cursor up. However for flying games I think of myself as the plane, so in order to mimic that movement the control stick then is effectively the plane. Inverting the left and right doesn't make much sense because that movement doesn't directly translate as well as up and down. Left and right inversion would be good for rolling not for pointing or moving in a direction.

It basically comes down whether you perceive yourself as the object or the one controlling a cursor.

Exactly what i am trying to describe. it's really hard to explain it without a visual example really. To me it just makes sense that way. But i guess each to his own preference in the end.

@ Da Cajun

That's exactly what I was trying to explain... thanks for the better description!