I was very surprised with this movie's 3D. Each composition is packed with depth and there are plenty of foreground elements and interesting sci-fi gadgets floating all over. The cinematography is great- the camera is rarely if ever static- the Steadicam operator is constantly but slowly shifting side to side for a 3D-enhancing motion parallax effect, and the use of wider angle lenses (than most films) gives the 3D a lot of room to breathe.
On the down-side, some of the layers are a little cardboardy. But you almost don't notice it, because there is so much to appreciate.
The other thing I didn't like (and this will differ from person to person and film to film), is that all of the shots of the monsters and mechs and other large-scale things, had what Del Toro claimed wouldn't exist- hyperstereo/miniaturization. In the real world your depth perception weakens as you get further away from things. In this movie, the depth stays pretty much the same with large-scale objects as it is with small scale close-proximity scenes. That boat that gets caught in the middle of the mech/monster fight at the beginning looked like a toy according to the stereoscopy, although other visual cues like the speed it was moving suggested that it was indeed a full size boat.
It's not a huge complaint, but if you're into realism, then these scenes do detract from the sense of immersion. I'm just mainly disappointed for Del Toro, because he was adamantly against this kind of imbalance in the depth at the time of the conversion announcement.