The CFA adopted by Fuji is no secret, there is nothing to understand, the problem is that apparently a demosaicing algorithm capable to render fine details without creating chroma errors has not been found yet and none of the provided compromise is, in my opinion, as good as it should be.
This is applicable to OOC jpeg, and to some extent to all the raw converters that are known to support the Fuji raw file.
Sean Reid has published a conpreehensive and well documented analysis on this subject which as been also covered by Sandy Mc Guffog in his blog.
The author of RPP has given up (so far) using any of his best performing algorithms and has provided VNG or a reduced resolution 2/3 as the only workable options.
The Author of Dcraw has done something similar, in the sense that whichever option you choose, the algorithm selection defaults back to a basic VNG.
Others such as Capture One, Apple, Raw Therapee, Iridient Raw Developer, Photivo, Photo Ninja ...have not provided a solution and in some case have explicitly declared they will not do because of the unconventional CFA.
This is not a very brilliant situation after so many months fron the launch of the Fuji X-Pro1.
May be soon the situation will change and I will be more than happy to recognize that I have been too pessimistic.
Having said that I think that, after the FW 2.0 release, the X-Pro 1 is a very nice camera with a huge, partly unexploited, potential.