Well things have moved on since the original post both in models released and the tech available.
Whilst I still am in favour of the OP's concept as I love having a shutter speed dial and aperture dial that work properly there are alternatives out there.
The Fuji x100s & X20 have answered a lot of the questions as far as fast AF goes, both employing a hybrid system with both contrast detect and on sensor phase detect, the combination has given them very fast focus speeds.
As for the OP's concept it was pretty much realised with the X-Pro1 as it meets most of his criteria,the AF speed has continually speeded up with body & lens firmware updates the future updated models will no doubt feature the same focus system's as the X100s and the manual focus has been much improved over the original X100's slow effort.
Direct access to ISO is via an assignable Fn button or the rear Q menu, though I would still love to see an ISO dial on the left hand side of the top plate.
Auto ISO? Not interested, it comes with constraints such as not being able to use manual exposure compensation in manual mode, you need to be in a set ISO to be able to adjust the shutter speed or aperture to compensate your exposure otherwise the auto setting just shift the ISO to compensate for the setting you use and you get a "correctly" exposed image rather than one with the exposure compensation you want.
Yes it can be handy on a changeable day with fluctuating light levels but its not important to me personally.
Manual focus though not as bad can be sidestepped by using an adaptor and various manual lenses, including Leica's, so thats really not an issue.
For years I'd longed for a digital version of the nikon FM, the X-Pro1 is the nearest I've found to it so far.
I also still think if fuji came out with a retro styled DSLR with top plate controls such as shutter speed dial and aperture rings on the lenses it would sail off the shelves.