To get back to very simple basics, when I did a comparison between the D3 and 5D some time ago in Bangkok, the first thing I noticed when I converted the RAW images from both cameras in ACR, was the obvious difference in color and hue in 'as shot' WB.
For the purpose of comparison, it was not difficult to get the color and hue very similar by equalising the temperature and tint in ACR. There was never an exact match, but globally it was close.