I used to use a Nexus D100 system and moved to the Sea&Sea D200. I already had Sea&Sea strobes.
One of the main reasons is the ability to use the TTL converter without issues. Have been hearing issues all over the place with using the converter with Nexus housings. I just got the Converter III and will try it out this weekend. I haven't got the D200 system wet yet, so I can't tell you how it would be underwater. Looks very promising topside though. The TTL is compatible with the strobes and hence I don't have to change them. To get TTL with Nexus (not using the S&S converter), you'd have to go with optical TTL via the Inon's. The S-TTL mode of the Inon is doing that, and hence I understand it works only on macro, as you'd need the strobe pointing accurately at the subject. You'd also have to fire the on camera flash. With the S&S there's no optical port, so this is not an option.
The other point for me is the availbility of other 3rd party manufacturers making compatible products for S&S. One thing that sold me was the Athena optical dome port (now sold by S&S). I got a very good price when I bought it in Japan. I didn't like Nexus' port strategy as they were producing ports made only for specific lenses. The Athena takes just about any WA lens/zoom that I'd ever use 10.5, 10-20, 12-24, 10-17, 17-55, etc by just adding extensions. Athena used to make this dome for Nexus, but I think they stopped recently. Athena also make a good macro port for the 105VR which I will upgrade to in the future. It has the capability to use Inon 67M close up lens. I also found a comany (F.I.T.) that made a zoom ring form my Sigma 10-20 which S&S did not have. On the Nexus, I used the 17-35 gear made by Nexus.
The S&S Port opening is also quite large, making it easier to push the lens release button when you have a gear attached. The S&S uses a bayonet type port and chunky o-rings: You have to push down a bit to turn it. The Nexus uses threaded mounts, which were easier to turn.
I also like the S&S black alumite coating which should wear out better than the painted Nexus. I also like the black color vs the silver Nexus, but for Canon housings, they make it all in black.
Camera install in the S&S is also very simple as there is a tray that you mount on the camera and perfectly aligns the M-S-C switch. On the D100, I always got this misaligned and had to reposition. The D200 Nexus also didn't have this control, which I use quite often.
The S&S is also a smaller housing than the Nexus. Good for travelling, but when I tried it inthe pool it was very negative. I had to whip up a home made float which helps lightenting it in the water, but I want to try to see what happens at depth.
On the mechanicals, I think that Nexus is of a better quality. All the gears and pinions are made from aluminium. On the S&S they are plastic. The controls shafts are also skinnier on the S&S. The shutter release is spring released, whilst onthe Nexus D100, there was no spring and you had to manually flick up to disengage.
No bottom tripod mount thread on the S&S. The Nexus had 3.
I don't remember what the viewfinder was like on the Nexus. The new ones have the multifinder lens. The S&S came with a 0.6X which expands the view, but makes the image smaller. There's also the 0.8X pickup lens which should be better for macro. But since I've seen companies offering to mount the much better 45 deg angle finder to the S&S I may eventaully go this route, making it equivalant to the Nexus option.
The S&S also came with a built in leak detector, where the Nexus doesn't have one.
Hope this helps! Sorry for the long note. Sounds more like a review...