Warning: Take the following with a large grain of salt. I do not think that this will have a very high chance of actually occurring but might just represent one possible avenue for Sony to develop their Alpha system.
I have already made a few predictions about what I expect and hope the Advanced Amateur camera will be like. I will make a few predictions about what the Flagship camera may be like when it is rumoured to come out some time next year, possibly at photokina. The primary focus will be on the sensor. I do not think that the sensor in the D3 will be used in a Sony body. The conventional readout using 12 high speed ADCs does not fit in with the sensors that Sony are developing. The coyness of Nikon to name the manufacturer also indicates that Sony has had very little input into the sensor.
If the size of the Flagship sensor is as expected (36mm x 24mm), I expect that it will be based upon the IMX021 and thus would be 28MP with a pixel pitch of 5.49 microns. It would have column parallel ADC readout giving 7fps if a suitable mechanism is found for AF and AE, either by a suitably beefed up reflex mirror or Live View. It may deliver 14 bit RAW files, not neccessarily because the DR warrants it but because of marketing concerns. Super Steady Shot will be included, the PMA presentation reinforced Sony's committment to providing this. There are no show-stopping problems in implementing this for a 135-sized sensor, merely a matter of mass, power, sufficient image circle (135-format lenses tend not to have a perfectly sharp-edged 43.3 mm image circle but have sufficient margin to allow for sensor movement) and control strategy.
Several shooting modes would be available, including a 7MP 14fps mode, either cropped to APS-C size or a subsampling of whole frame. These would be in Live View mode. A selectable 12/14 bit RAW file would also be provided. For single shot mode, a high precision sampling option would reduced frame rate but possibly justify the 14 bit RAW file. It's pretty safe to say that the image buffer will be large, possibly 1GB giving 20 RAW or 100 JPG shots. Sony may use a DNG file format, losslessly compressed. Other possible features are weather sealing, 100% viewfinder, interchangeable viewscreens, wireless transfer and control, and geotagging (GPS).
With the Flagship, Sony will want to make a strong statement. By providing the highest pixel count in a 35mm-style DSLR, Sony would signify its committment to the Alpha mount. Coupled with Zeiss optics, the combination would be a serious professional set-up.