The extended edition only being with the 3D version really annoys me. I understand it's on one of the 2D discs, but it still sucks for people who want to see the EE but don't have 3D. You shouldn't have to pay extra for something you don't have any interest in to be able to see something you want.
I also hate it when on the disc there is bonus material that I never watch. Can't I get just the film and pay less?
They do sometimes release "bare bones" DVDs that are just the movie. Or if you don't mind not having a physical copy, there's always digital downloads.
I'm very curious to see what they'll do for Wolverine 3 or The Wolverine 2, whatever you want to call it. Is the two year gap you guys are talking about between The Wolverine and DoFP or The Last Stand and DoFP?