CCD vs. CMOS doesn't relate to color and probably also not to tonality and DR. Both sensor types simply detect photons. Early DSLRs were mostly using CCDs and they mostly had AA-filters.
Color is dependent on CGA (Color Grid Array) and not on CCD vs. CMOS.
I don't argue about implementation. Very well possible that some vendors make better compromises than others. Phase seems to put a lot of effort in individual calibrations of their backs and they may capitalize on that with Capture One using proprietary information.
It is very probable that DSLRs are biased to high ISO performance. The choice of CGA (Color Grid Array) may be affected by that, leading to some "color blindness" on some DSLRs. There was an article on DxO-mark comparing color filters on recent Canon and Nikon cameras detecting some color blindness on the Canon.
It seems that Sony's Alpha 900 has "better color" than the Nikon D3X, although both use a similar Sony made sensor. The Nikon has better high ISO characteristics but is said to have less good color. This may be a design compromise in the CGA. Nikon probably has better processing pipe line (14 bits against Sony's 12 bits) making for better DR.
Lenses matter a lot. A good lens will transfer more contrast for fine detail. MTF falls almost linearly with frequency, so a sensor with twice the size will have twice the "microcontrast", add to that a very good lens and an MFDB has a real advantage. The Leica M9 doesn't benefit from sensor size but their new lenses designed in the "Kölsch era" seem to be truly excellent designs, the "Mandler era" design are according to my understanding closer to main stream.http://www.imx.nl/photo/optics/optics/page93.html
CCD doesn't do high ISO or live view or video. Lack of AA filter can lead to moire (not as much of a problem as in the days of 9 and 12 micron CCDs but still an occasional annoyance).
99% of consumers (and that is market that the vast vast majority of what Canon/Nikon sells to by revenue) would not be willing to make that compromise for the better color, tonality, DR, and overall image quality.
It's that simple.