I agree that 3D did little to enhance the experience of The Avengers for me. Pretty much the only movie I've completely enjoyed in 3D was Avatar, because it was intended to be shot that way - and because it was a truly majestic panorama of a completely alien world.
But for The Avengers, I went and saw that in 3D twice, then again in 2D. And realized I'd overpaid the first two times. I might've used that cash for a bigger container of popcorn, or another box of candy. Really, I don't think they've nailed the usage of this technology yet, and it gives me a headache. The glasses are irritating (primarily because I already wear glasses, and wearing two pairs hurts my ears), and while I'm wearing them, I don't feel any more immersed in the world being presented than I was before.
Bottom line: they're over- or under-applying it to too many movies out there, and it needs to stop, or people like me will wait even for the blockbusters to hit the racks so we can avoid the usually awful murk of unnecessary 3D rendering.