3D also usually monopolizes the best (tech) screens/sound systems.
I'd pay the 3D fee to get in the most modern 2D theatre experience possible. I also get frustrated that 2D showing times can be quite limited if I want to see it on a system better than what I have at home.
There's always an option to bring 2D glasses [1] to a 3D movie showing.
[1] Not a joke: on Amazon you can find polarized glasses that work with most theaters where both lenses are polarized to just a single camera (left 2D and right 2D). I've got a friend that experiences motion sickness at 3D showings that uses them to see movies where everyone else wants to see 3D. One of the lesser utilized but awesome tools with some of the home 3D TVs (like my LG) is to have one player with left 2D glasses and the other with right 2D glasses and play a "full screen" coop game.
I'd pay the 3D fee to get in the most modern 2D theatre experience possible. I also get frustrated that 2D showing times can be quite limited if I want to see it on a system better than what I have at home.