The unique element of pixel binning with Sensor Plus technology is that while resolution is reduced and sensitivity increased, the user still experiences coverage of the same area of the sensor, ie; the entire sensor, not a reduced area of the sensor. Also, because we implemented the process before the A/D conversion, we eliminated the issue of exponential noise to signal ratio that has traditionally been the downfall in terms of image quality.
The latter is a good point, although I am not sure how often it would have been an issue. As for the former, I am not sure which pixel binning implementations you refer to which didn't use the whole sensor.
I recall reading a series of articles about how to use multiple images and Photoshop to achieve higher resolution (stitching), greater coverage (panoramas), greater dynamic range (HDR), lower noise (pixel binning), and so on. There is a lot more software out there now to support the various workflows, of course, but without wanting to criticize the development of Sensor+, I find it hard to imagine that this is a do-or-don't feature for anyone. It would make life easier for a few people, but simply downressing a 60MP to 15MP image in software would probably get you 95% of the way there. The rest is very incremental.
Honestly, and I am not pointing at Phase One only here, the advances in medium format digital in the last several years have been so minimal, mostly focused on higher MP counts, slight increments in convenience, and higher ISO performance. The whole field has been relatively stagnant for quite some time, and I don't find it surprising that the general tendency is downwards. The Leica S2 is about the first really interesting camera in MF for quite some time (and the arTec a bit too), and I think that this may be the first camera in 10 years which has the potential to grow the field, rather than just staving off the shrinking. The combination of 35mm handling, size and weight, and MF quality has the potential to change how high-end fashion studios work. Hopefully the software falls into place too, and the service end works out.