I won't try to delve into the technical aspects of either camera, but I do want to mention that I happen to have both the D100 and the S2 Pro. Yes, by far, the S2 Pro takes more pleasing photos - read better balanced here - right out of the camera than the D100 does. It is a beautiful instrument, but then...so is the Nikon D100. I at first cursed the D100 shortly after I purchased it, but as I continued to read various forums, I added to my database and learned to live with the camera. I made adjustments, experimented, and pleasantly discovered that the D100 custom tone curve scenario - using NC - was something that no other brand of camera had.
So I use both cameras, and loving the fact that I can interchange both lenses, flashes, and most nikon accessories on both. I give the nod to the D100 for overall adaptability, settings, and ways that one can customize the camera for a particular shoot. I give the nod to the S2 Pro for overall pleasing photographs in color, balance, and definition, along with great flash photos using any type of Nikon dedicated flash - not just the DX flash units. Honestly, I love both, but do tend to reach for the S2 Pro more often than not - at least lately. I purposely push myself to use the D100 as often as possible and am playing around with different custom curves.
It's your call. Either choice should work out well.