I always play with inverted, partly because I've played a lot of flight sims, and partly because it's the natural, 'proper' way of aiming.
Think about it, if you're holding a rifle, you're mainly gripping it by the stock. If you want to aim up, then you move the stock down, which tilts the barrel up, and vice versa.
Unless you hold a gun by the barrel, then inverted is the 'proper', natural way of aiming.
The up/down movement in FPS games is relative to part of the gun you hold, not to the end of the gun the bullets come out of.