A few weeks back I had been looking for a compact system to complement my 5D MKII (for when I didn't want to carry a big, heavy kit) and weighed waiting for the Fuji X-E1 vs the Olympus OM. I decided to go with the Olympus because of the demosaicing issues that had been raised using Lightroom. Although the RAW conversion with the supplied software supposedly avoided these issues, I do my conversions in Lightroom and didn't want to deal with a new piece of software. I am just curious as to thoughts (as noted in Alan's post) about this particular issue and how important it might be, as I have never used the Fuji or tried to convert it's RAW files (though I have seen pretty convincing examples on other sites).
It's been interesting that so many reviews don't bring this up, since it is a common topic amongst users in various forums. Lightroom certainly seems to be the worst at handling X-Trans files at the moment, but, there are still issues with the supplied camera software and in-camera jpegs when it comes to smoothing at low to medium ISOs. In a nutshell, chroma smoothing is inherent to the CFA scheme, so, while this sensor certainly is tops in regards to high ISO performance, even bayer 16mp sensors WITH an AA filter have higher chroma resolution and overall better performance at low to mid ISO, so it's a trade off. Plus, that is assuming ideal raw conversion, which we don't have yet, because it would take a complicated, multi-pass conversion process.
It seems that the fantastic low light performance of this sensor has reviewers glossing over the performance in good light, where other sensor options are better. While some love the performance of X-Trans, others are refraining form buying into the system simply because of the new cfa and its trade offs.