I am not sure since Avatar was one of the few films I had to watch in 2D. :D But I don't think there's any particular reason why a 3D film ends up being darker:

I am not sure since Avatar was one of the few films I had to watch in 2D. :D But I don't think there's any particular reason why a 3D film ends up being darker: the cinema people simply need to raise the brightness of the lamp.