I thought the 3D in Guardians of the Galaxy was very, very good. Director James Gunn shot the movie with 3D in mind and there was a constant sense of depth and quite a few pop-out moments (debris, business ends of various alien weapons, etc.). The movie is a post-conversion but since so much of the film involves green screen and CGI it was probably a lot easier to get a pleasing 3D presentation and Gunn goes for an often aggressive 3D image with very visible separation between foreground and background objects.
While I agree that the 3D in most Marvel movies is bad, and that Captain America 2 is particularly forgettable (especially after how Captain America: The First Avenger was such a good 3D conversion), Guardians is definitely in a different class. In fact, the Captain America 3D BluRay actually has a 3D trailer for Guardians and just from that you can see a dramatic difference in the quality of the 3D.