I thought the 3D was on the conservative side: moderate depth and very minimal pop. Even though the movie was often quite dark, I never had any trouble making scenes out even with the glasses on and ghosting was completely nonexistent on my 2010 Samsung plasma.
As to the movie itself, I saw it at the theater and liked it but was not blown away by it. That was pretty much my reaction when watching it again at home. Interestingly, the deleted scenes (only visible on the 2D BluRay disc) are far superior in my opinion to the what we got in the finished cut. An alternate scene of a far more alien looking Fifield (in which his melted helmet harkens more closely to the translucent dome of the original alien) attacking the crew and alternate ending where Weyland speaks to the engineer and dares compare himself to a god were far more interesting than what we got in the actual movie. There's also an interesting scene between Janek and Vickers wherein Janek relates a story from his days as a soldier which nicely summarizes the what the crew has discovered (it feels far more organic and smartly laid out than the scene in the film where he tells Elizabeth that the planet is a giant weapons station). The alternate scenes of Elizabeth confronting the engineer and her final conversation with David are also far more interesting and thought provoking (and also tell us exactly where they are going in the alien ship at the end).
In watching the excellent documentary on the making of the film it becomes pretty obvious that Ridley Scott sometimes outsmarts himself as he comes up with idea after idea while in production and I think he sometimes doesn't know when to leave well enough alone or what is dramatically satisfying (shades of his decision to cut the cocoon scene from the first Alien). If he'd left some of that excised footage in the movie I think the final experience would have been far more enjoyable, interesting and relateable to the original Alien.
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