I thought the 3D was pretty great, there were a handful of scenes where stuff was flying right out of the screen at you, and really enhanced a lot of shots that were right from the '95 film. It was also crystal clear, I can't remember the last time 3D was so in-focus, usually I'm adjusting my glasses the whole film.
Yeah, a few shots during the Deep Dive had some cool 3D effects. Also during the Spider Tank fight.
But overall? I don't think 3D added anything to the movie.
GitS is a great looking movie.