They are fairly flat and I'd imagine they'd work with your glasses although not perfectly. I wear contacts so I can't swear to it, but I've worn glasses with 3d glasses in the past and was OK if a little awkward.
Loved the movie, but I agree, I don't know how much "extra" 3D really brought to the table. First 20 minutes of the movie was kinda boring too, well, not so much boring as much as it was not really needed.
Ultimately decided to see the 3-D version based on comments from my brother about it not being an issue. Felt a little funny at first, but I had no problems at all, and I suppose it does make sense that the people who make the glasses know that an awful lot of people wear prescription glasses and would need the 3-D ones designed to accommodate them.
I very much enjoyed the movie, but I also understand why people who aren't Tolkien devotees might get bored or frustrated with the beginning. There's a lot of backstory and exposition relating to the history of the Dwarves that would likely leave the casual viewer a bit frustrated. I also wasn't too thrilled with the portrayal of Radagast. Nothing to do with the actor per se, just the way he was portrayed as a bit of a buffoon. He wasn't in the book, but he does make a very brief appearance in the Lord of the Rings when Gandalf encounters him on the Greenway en route to meet Frodo at Bree; Radagast warns Gandalf that the Nazgul have been seen west of the Anduin. The portrayal in this movie made him out to be a total flake. In the book, Saruman ripped on Radagast, and he does so in this movie too, but since the viewer presumably knows, from the other three films, that Saruman is not to be trusted, it's unclear why the producers went with that characterization.
But that was a very minor issue.
I'm glad I saw it in 3-D because it was the first "modern" 3-D movie I'd seen, but I agree that it was hardly vital. Still pretty damn cool in a couple of the fighting scenes, and I thought Gollum's cave was well-done in terms of the 3-D aspect. I thought this would be an ideal one to make my first "modern" 3-D movie because I know the story so well, meaning that if I missed something because I was paying attention to the special effects or the 3-D it wouldn't be a big deal because I'd pretty much know what happened from having read the book many times.