lol - I hope you had better luck than me.
(I had a headache 10 minutes in.)
The problem, I decided, came down to the weapon model. I have no trouble watching 3D movies - but when, say, the AR is taking up the bottom chunk of the screen, my eyes were trying to focus both on the very close and the far-away at the same time, and it didn't work.
If I switched to a smaller weapon (say, the pistol), things were better - but that's not really a solution. (I never got my hands on a rocket launcher in 3D mode, but I'd guess that would be terrible.)
Eh. Halo Anniversary is gorgeous in 2D. I don't need the 3D.