In general I will still say that the best RAW converter is the one you are most familiar with, also with X Trans files.
All raw software developers do different trade off's and one can not say in general that one converter is better than an other, it all depends on the subject
and in fact on every single file.
The latest normal Bayer sensors, for instance the ones from Sony, can withstand a lot of rather aggressive sharpening to bring out a lot of detail.
With the Fuji X trans files I do not see an advantage in detail recovery compared to those. And if you manage to get out a lot of detail it is also with a lot of artefacts mostly.
For my workflow I like Lightroom the most. But for X-Trans landscape work the results are mostly too soft or I start seeing a kind of paint brush effect that I do not like. With Photo Ninja I might get more detail out of the files, and foliage looks more natural. But depending on the image there are also color artefacts popping up that I am not able to repair without degrading the image in another way. Programs like Capture One and Aperture are somewhere in the middle regarding trade off between detail/sharpness and artefacts.
So for myself I would be very happy if Fuji would leave the X-Trans technology because I like using some of their camera's. I would prefer they opt for general Bayer sensors perhaps without anti aliasing filter but with higher pixel density that allow oversampling with a choice of actual pixel output. That is at the present state of sensor development.