As for the Hobbit, I had problems focusing when I watched the Hobbit due to my old contact lenses irritating my eyes (note to self - new lenses before the cinema!) ut from what I could tell the 3D was tasteful, much like in Prometheus, focusing more on depth than scare tactics.
I have not really watched many 3D movies though. Alice in Wonderland is the only one I disliked the 3D effect in, can't put my finger on why.
Dredd 3D however did a good impression on me. The 3D was used more to intensify (?) the death-scenes and the use of the slowmo drug in a somewhart artistical way. To this date I think it's the best use of 3D I have seen.
I would LOVE to see documentaries that utilize 3D, but also more artistic use of it. But as with everything else, taste differs from person to person.
In the end however, 3D is still a new technology and it's not just the audience that has to get used to it, but also the people who make the movies. I say it might be worth while to give them another year or so before getting rid of it - Because if used right, 3D can be a pleasant addition to a movie.