Jorgen,
this is exactly the point, the H3D2-50 with standard lens is far better in resolution, flexibility of the system and SW and has a proven track record, whereas the S2 is more expensive, less resolution, less flexibility and has no SW coming with it (I am talking about manufacturer generated SW like Phocus or C1Pro) and the support and the reliability of the S System is just in the stars for the next couple of years.
Far better resolution is to overstate it a bit. The Leica sensor is around 7500 x 5000 pixels, while the Hasselblad is 8176 x 6132. That means that the Hasselblad sensor with regards to pixel count is 9% wider and 23% taller (the Hasselblad has an aspect ratio of 4:3 and the Leica 3:2). But if the Leica lenses are better than the Fuji lenses, that advantage may fast turn into dust.
There's obviously more options available for the H3D. The camera that it's based on was launched seven years ago, while the Leica isn't yet on the market. But that also means that at least parts of the technology in the Hasselblad is seven years old.
Obviously, there's a risk buying new technology. I believe some of those who bought the first cameras in the H-series had some experiences they could well have been without, not to mention the situation that arose when Hasselblad launched the H3D and closed the door to the past, and to the future for many H2 owners.
The fact that there's no proprietary software available for the S2 has nothing to do with the price, but with the usability of the camera. For many photographers, this is a big issue, but for others, it's not. If the camera sells, and I'm more than convinced that it will, software will appear that can do the job.
As for flexibility, it also depends on what glasses you wear. For me, flexibility means having a camera that is ready when I am, is compact enough to carry anywhere, and can live the life that I live. Even getting through customs in some countries I travel to is difficult if you carry something that doesn't look like a "normal" camera.
The professional photographers of the future doesn't know what a darkroom is, and probably take their first photos with a Nokia. To them, a traditional MF camera is ancient technology. The alternative for them won't be a Hasselblad or a Mamiya, but a Scarlet. That's the flexible solution for the future, for studio, for landscapes and for video too.