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Flashinm, assuredly, as raw converters get better, the Trans-X output will get much better. According, to Joachim, though, even in a perfect raw conversion, "The Fujifilm principle will in any case never get better than 50% of the Bayer chroma resolution, an inherent property of the scheme. At higher ISOs this turns into an advantage in stead of a disadvantage." It's simply a trade off, but it may not be enough to worry about.
Frank, it's really tough to say which camera to pick, based on output. You may find that the high ISO improvement outweighs the low ISO occasional issues. For me, I'm sticking with bayer, at least for the time being, which, as an X100 owner, kinda stinks, because I certainly want to like the new Fujis.