I'm on my fourth X-trans camera (the X-T2) and I agree: Fuji would have saved themselves and everybody else a lot of work if they had just used Bayer sensors from the beginning. Endless discussion threads, probably stretching from here to Alpha Centauri, could have been prevented.
Before my first Fuji camera, the X-E1, I had the Nikon D7000 - both of them had the same (or very similar) 16 MP sensor. There was no discernible advantage or disadvantage between the raw files from the cameras. From what I have read, it appears that X-Trans sensors might give slightly less colour noise in high-ISO images, at the cost of needing more processing power. The difference seems to be negligible. All modern sensors have impressive dynamic range compared to my first digital camera, the D80.
On the other hand, it should also be said that Lightroom's rendering of Fuji raw files has improved greatly. Today, there is absolutely nothing to worry about if you use Lightroom and X-Trans. For ultimate sharpness you might want to run your raw file through the Iridient plug in (assuming your image is perfectly focussed to begin with), but for me Lightroom is the most practical all-round program. It does not excel at one thing, but does so many things so well that I prefer to use it (highlight and shadow recovery, purple fringing removal, the look of high-ISO noise ...).