I have used both brands extensively in the last few years and recently made the choice between them (and others) when selecting a housing for my D4.
Neither would be a poor choice. In fact I believe that they are both in most people's top 3 choices, money no object.
In terms of ergonomics (ease of using your camera underwater) I believe that they are strongest two on the market. Nauticam continues to innovate and if you look at the ergonomic features and solutions on their D4 and D800 housings and compare them to any of the Nikon D3 housings on the market (Nauticam didn't make a D3 housing) then the progress is, quite frankly, amazing.
The number of controls that have been moved from being push button to being conveniently positioned levers in impressive. As is the Nauticam multi-selector. Plus you've got port lock, great viewfinders, excellent housing latches and a full port and accessory system.
The but comes with reliability. And this is a sensitive issue. First because when comparing brands we tend to exaggerate the differences for the sake of comparison. And second because there is a difference between what photographers will say face to face compared with what they will write on a forum. People have even said to me that they dare not speak out against some brands on Wetpixel because they know the dealers are reading!
But you would have to live with your head permanently in the sand (or underwater) to not have seen a Nauticam niggles threads. Though it should be stated that there are also a lot of Nauticam's out there now. There is one below this in this forum:
http://wetpixel.com/forums/index.php?showtopic=48174
That said, I haven't had a problem with a Nauticam that has stopped me shooting. I think that most issues we see are best thought of as housings going out of tune. It is worth budgeting for a service every year or two and you will be insulated from these. Plus the dealers are excellent at staying on top of them. But I have had niggles with the controls on my Nauticams. I have never had a Subal serviced.
In the end I chose a Subal for my Nikon D4 (not just over Nauticam - I considered many brands). There were many reasons for this. And yes, it was not as financially attractive as some other brands for me!
But one important factor was that I dive and shoot and the Subal's I have owned have been trouble free.
Ergonomically, I was attracted to the fact that the Subal D4 had three controls I had not seen on a housing before (Pv, Fn & AF-ON(vert)) all of which are programable. I have written else where on how I can now shoot silhouettes for example with the pull of my right finger. It is a big step on from their D3 housing. And they have focused development on improved ergonomics (moving controls) and improved reliability, beefing up controls that have caused problems in the past and keeping engineering solutions simple. They have also introduced an ISO lever, which was something that Nauticam introduced on their D4 housing.
Subal now have a port lock, although this isn't a big issue for me, first I've not had a problem with Subal ports (although have seen others) but also I have a vacuum seal on my housing, which checks for leaks (pre-dive) and holds ports firmly on the housing.
I realise that I am not your typical underwater photographer. Shooting a huge amount more than the average. And therefore for me ergonomics and reliability are super important, while for others who dive less regularly all housings are already over engineered for their needs.
Alex