I'm gonna say no to 3D. The only reason I saw it in 3D was because it was the only none sold out show.
The movie was not filmed in 3D. The 3D was an after thought just like almost every other 3D.
There have only been a handful of movies that were meant for 3D. Most of them being animated. Avatar sets the standard for me. And Avengers doesn't even light a flame compared to that. At no point did feel like something was coming out of the screen at me.
So IMO just stick to 2D. You're not missing anything.