I have both lenses and I don't think you can go wrong with either. I have done pool tests with the 16-35 but not actually used it in a shoot, I do plan to next week. My sense is that underwater this lens will definitely perform better without a diopter with better edge sharpness behind a dome than the the 17-35. If you add a 3-4 diopter to the 17-35 than the edge sharpness will probably be a wash, but then you lose some angle of view so for similar performance the 16-35 will be noticeably wider. Topside you'd probably have to pixel peep to tell a difference in sharpness. I think this lens will prove to be sharper and perform better under rigorous testing on digital cameras; remember the 17-35 is really a lens that was designed for film so issues like light divergence etc are probably better managed in the new lens, how important that is I don't know. I think the extra stop on the 17-35 is only of potential value topside, though not something you are likely to need much with the D3x or D700. I think the only advantage of the f2.8 is if you need more out of focus background effect with the 2.8 vs f4. As regards ability to shoot low light, the VR more than makes up for the extra stop.
The 16-35 lists less than the 17-35 though you can probably get a better deal on the 17-35 now. My verdict, if you can get a real good deal on a 17-35 go for it, otherwise buy the 16-35.
I think I will probably sell the 17-35 at some point, but I love that lens, so find it hard to let go just yet.