This thread is interesting in that the Godzilla message board I frequent just went through this SAME experience of the Godzilla (2014) 2d vs 3d bluray differences with people being very upset that the 2d version was noticeably darker.

But what a lot of people don't seem to realize is that 3d copies are almost ALWAYS a bit brighter in order to compensate for the fact that 3d glasses have a slight tint to them. You can't compare a raw 3d screenshot to a 2d screenshot. To make the comparison fair, you'd need to send the 3d shot through a filter equivalent to viewing it through the 3d glasses. And I'd be willing to bet that if you do that, they will look awfully similar.