The D600 has had a known issue with the sensor; recently a class action suit was filed against Nikon, and the judgement was that Nikon needs to repair those units and Nikon has recalled them. i believe by doing so, you will be getting the new D610, which is an excellent upgrade. I do not see the D610 vs. XT-1 as an either or - they are both excellent, but different, and the D600 will still produce superior images due to its sensor characteristics. I love my XT1 and I love my Nikon D700, and D800. Different tools is all.
Based on the latest Fuji x-lens roadmap, the next zoom(xf16-55 f2.8) is due in the first quarter of 2014, so it could be any day now. If you have no desire for one of their incredible prime lenses, it would make sense to wait for the zoom. Otherwise study the ones already on the market and balance the future usefulness versus cost to help decide which one to get now. The 35mm f1.4 would be hard to beat in the value/utility equation and is also of top quality, so if you can't decide, I suggest that one.
Skin tones from the XT1 in my eyes seem to be right on. I cannot compare the S5s or the Nikons as I have not shot a Nikon in years nor the Fuji S5s. Coming from a Leica M8 which always rendered skin warm I can say the XT1 is very natural to my eye.
I believe the camera can do three exposures: your then current setting, plus two others, including Auto Exposure, ISO, the film simulation modes, etc. I don't think it has a infrared mode, but I could be wrong.
Yes you can set it up to do everything on auto if you want and its still easy to change everything yourself if you want to.
The best thing about the camera is how small and how well it feels in the hands.
Yes, you can use the hot shoe to sync with a variety of external flashes... There is one that comes with the camera but that one is just for emergency use in my opinion. I am currently using Yonguo flashes and triggering them with an optical trigger. It works like a charm....