The gopro 3D works best with closer objects but thats similar to how our eyes actually work too, you do lose depth perception the further images are as your eyes are a set distance apart and we dont have any zoom with our eyes or at least I don't lol. As most 3 dimensional depth perception is for objects not that far away this works great underwater as generally we are limited to the distance we can see anyway to 5-40m depending on conditions so everything in the frame is relatively close compared to when doing other land based activities.
The main difference though is that human eyes turn in to see closer objects the same as other professional 3D systems, the gopro is a fixed lens and you cant adjust the physical lens angles in any way so your not getting the optimum 3D experiance, this can be adjusted in software to within certain limits that you must understand when using the gopro for 3D images.
However for what the Gopro is designed for being a wearable sports camera to capture cool videos and images while doing things that its not practical or possible to bring any other camera, its a basic point and shoot setup and many uses of the gopro you dont have any time to adjust camera settings mid action so a proper pro level 3D system would be impossible to use properly anyway.
This also makes the gopro 3D very easy to shoot but you need to work out the limitations and at which level can correct these issue in software to make the 3D effect work and avoid eye strain for the viewer.
I think for what it is it works well enough and some cool video can be made using this setup, your not going to film Avatar 3 with a gopro but you can make something pretty cool that not many cameras are capable of, its still one of the smallest/toughest 3D camera setups available that can be used in ways not many other cameras can be.