From what I have seen of CMBN in videos and read in AARs, I don't think there is any real point comparing the two games anymore.
Sure, they both play very differently, but that is perhaps not the point. One game clearly has had a lot of money invested on development of the code and graphical assets. The other has had exactly nothing ($0) spent on it, and sadly it shows. Now of course Matrix is giving away their game for free for the most part. I guess they really had to do this otherwise they would have been seen to be making money off the backs of a lot of volunteers hard work.
And boy did those boys work hard! I know! But still they all had day jobs, and work was done on an "interest only" ad-hoc fashion without any Matrix leadership input or a even a cohesive design plan.
Bottom line is if you are lucky enough to have money and time to play both, then great do that and enjoy. But if, as I suspect, most of us only have time (or money) to devote to one game "system", I strongly suspect you would be better off with CMBN.
All IMHO (as the coder of PCO).
S