The only issue i have with 3d as of now is the focus point. Its not on everything i watch, mainly the documentaries, watched Transformers last night with no issue at all.
Let me explain what i mean. In a 2d movie, if i want to look around on the screen, there is nothing keeping me from doing so. If the focus point is in the foreground, i can still look around and see the background. In a 3d movie, due to the depth, and the fact that the cameras focus almost MAKES you look at what it wants you to, i find myself getting frustrated that i simply cannot get certain things to focus.
This may well be a convergence issue, but to me its just frustrating, i like seeing popout, but it distracts me when the popout isnt what were focusing on in the movie, then i try to look at it and cannot because it isnt in focus.
Then again, this may just be my ADD talking