I'd put my money into the 16-35mm f/4 IS L. I've owned a 16-35mm L II in the past, and currently have a 17-40mm L (*but have not yet had a real-world play with the new 16-35mm f/4 IS L).
Whilst the 16-35mm f/2.8 L II is quite good optically, the f/4 seems to beat it in all areas. Sharper, and with less diffraction/chroma/distortion in the corners etc...
I quite like the reviews on this site, and these 100% crop comparisons are good for pixel-peeping comparisons (but not so much for checking real-world things like flare characteristics or bokeh quality, though there is even some samples covering those too!):http://www.the-digital-picture.com/Revi ... &APIComp=0
I would argue that IS really only extends the time you can "hand-hold" a shot, so while the IS will help prevent camera shake, it isn't going to prevent motion-blur of your subjects if you're shooting portraits/people-pictures in low light or indoors. In those cases, the f/2.8 may be the (technically) better option as more light getting in will mean a shorter shutter speed for the same amount of light, which in turn would mean less motion-blur of any people in frame. In really low light it does require a very steady hand though, and you're likely to still be cranking the ISO well up. I'd hazard a guess that shooting low-light, handheld, no-flash indoors portraits is likely to be a very small component of what you want the lens for anyway? And if you really wanted to push down that road, a fast-prime with a f/2 or wider max aperture would likely be a lot more practical for that type of low-light/indoors shooting if that's going to be a primary use for the camera/lens combination.
In my opinion, the f/4 IS L version will be a lot better for pretty much every other scenario anyway, and that with the change to the 6D, winding up the ISO another 'stop' may not be the end of the world for the odd occasion you have to push the limits of the combination in low light anyhow.
One often overlooked feature of these types of lenses, the f/4 IS L version has a 77mm filter thread - which is shared with many of the other Canon 'L' zooms. The 16-35mm f/2.8 L II and 24-70 f/2.8 L II being the odd ones out that require 82mm filters (which are often significantly more expensive, or require an extra adaptor ring to be carried for plate-type filter holders). This means if you're pairing up with something like the 24-105mm IS L, you can swap filters between lenses to save a few dollars (though no time!). The 24-105mm gets a vote from me too. I don't believe the 24-70's are all they're cracked up to be, and the focal range of the 24-105 makes it a really handy alrounder. After buying selling and trying a whole bunch of lenses in the 16-85mm range - in my opinion if you really want/need a faster aperture than f/4 in a sub-135mm focal length: Jump over to a fast prime - as f/2.8 isn't that "fast" an aperture in the wider focal lengths that you're going to get lightning fast shutter speeds or amazing subject seperation/bokeh anyway. Just my 2c anyway...
At the end of the day, unless you're predominantly shooting indoors in low light - The 16-35mm f/4 IS L is likely to be a much better alrounder, and best of all will save you about $500 off the 16-35mm f/2.8 L II.
One thing I do like with the Canon lenses is the waterproofing is extremely good. I used my 16-35mm f/2.8 to do a long exposure (or several, lol...) in the rain where the water was actually beginning to run down over the lens and camera and I never had the slightest hint of a problem from either camera or lens.