For some reason, it changes from game to game for me. After years of anguish in trying to figure out exactly what I DO want, I think I have a few ideas how my thumbs work.
Full-blown FPS: Not inverted
Adventure game: Inverted.
I had been putting some time into L4D, and it broke my bad habit of not being able to use dual sticks. I was quite happy and surprised that after all my gaming on my N64, rectified was my choice alignment. Then I tried out Kameo, and every time I had to aim with the icicles in the first level, I would move the stick as if I wanted it inverted.
My thumbs have played too many different games, and are too confused to really know what they want. Games like Jak and Daxter messed me up too, because camera control is reversed on the X-axis because of the third person camera. Switching to a FPS ended up being difficult because of pushing the wrong directions in just about every possible way. For the longest time, I just stopped playing console FPSs.