I just bought another D3x last week, they are damn fine cameras.
To cut a long story short, I sold my old D3x to purchase a P45+ but sold it since, hence the new D3x purchase, I honestly can't praise them enough.
My ideal D4x changes would be the following
1) higher resolution screen (it's fantastic now but needs slightly more resolution to get front to back sharp images with tilt lenses)
2) More mega pixels is always welcome, but never at the cost of quality!
3) ISO 25 would be a dream but seriously, ISO 50 would do me.
4) A long exposure counter would be nice!
5) Screw threads on both sides of the camera for tripod mounting in portrait/landscape orientation, this would save costs purchasing L brackets!
6) Rule of thirds superimposed on either viewfinder or live view screen would be nice but not essential, I like this as an aid rather than something to religiously follow.
7) Built in GPS that can be switched on/off.
8) 16 bit files would be awsome, but then so would 24 or 32
Those features would keep me more than happy for a long time.
As for 'diffraction' I really don't see this as a big deal, lenses, AA filters, sensors are so finely tuned these days, plus you can simply test your equipment and see the effects of diffraction on your screen within minutes, from there you can decide how much diffraction is too much for you, I:E print sizes, etc.