There are number of things; starting with the design of the port and extension ring locks - they are simple to use, quick, easy and work well. I know Subal now finally, has a port lock (but not an extension lock which makes the port lock ineffective), but I never had one with my D700 housing, and though I never flooded it, came close a few times, and saw it happen to others when the port twisted off. The controls mesh better, I found the Subal more finicky with getting every control perfectly aligned - particularly the focus mode control lever and frame speed mode control. Positioning zoom rings on lenses was more variable and more prone to slipping if not just right. Nauticam seems to simply lock into the housing more rigidly aligning the controls better, and zoom rings can only fit in one precise position.
External button and control positioning; Nauticam have gone to the trouble to place internal levers etc so that external controls can be moved to better positions on the housing - examples are the ISO control lever, and the other paddle controls on the right for mode etc - a much better solution than searching for the buttons on top or back of the housing, the focus point multiselector is moved more to the right side of the housing, not just directly above the camera buttons, so I can reach it with my thumb without moving my hand off the handle. Also the ring multiselector rather than four buttons is a nice touch. I have smaller hands, so these little things keep all the commonly used controls more directly under my finger tips. The use of paddles rather than buttons where possible is huge, a paddle is much easier to use than a button particularly when one has to hold it down while rotating a command dial. I found that I often had to take my hand off the left or right handle to hold down a button while I rotated a command or subcommand dial with my Subal - this would sometimes mean I had to sort of jam the housing up against my body to hold it while I accomplished a two handed control operation like ISO change. This does not happen when I have a paddle where I need it without having to move my hand. I would like to see even more paddles where possible rather than buttons. Lens release button works better, does not need to be swung into position etc to use. So overall, even though I was not unhappy with my Subal, I did not know any better and none of the other housings, at any price, including Seacam, appeared to be any better ergonomically. In fact, at the time Subal was the best housing ergonomically in my hands.
I think Nauticam have really shaken up the staid European camera housing makers and demonstrated that it is possible to continue to improve housing design. In all my previous discussions with European housing manufacturers at DEMA etc, there seemed to be a take it or leave it attitude to their approaches to housing design, particularly as I was not a professional photographer. Port locks on Subal are a perfect example, other things I never even thought of, like paddles and multiselector etc, just made for a better mousetrap when I never thought one was possible and I just needed to accept what I was given.