I've been using Capture One for my Fuji .RAF conversions since it first started supporting X-Trans files, and feel that it does the best job overall. You do, just like with Lightroom, have to spend some time really getting to know the app, and I've been working with Capture One 7.X.X for over a year now for my X-Pro1 conversions.
For my X-T1, I've been using Iridient Develpor and Aperture for my X-Trans files to convert them to TIFFs, whereupon I reimport them to LR for some minor post-conversion tweaks. On the whole, until today, that is, I found Iridient Developer to be the best, but I agree it's workflow could be improved upon; I really wish it supported a full-screen sized browser view like Photo Ninja or Lightroom, but Brian says he's focused on other priorities right now. I found Aperture to work pretty well, too, but I have observed artifacts with Aperture, also.
I just downloaded the latest rev of Capture One 7.2.1 tonight, though, and after using it on some landscape shots, still feel that Capture One still does the best job of RAW conversion I've used,
on any camera for that, matter. I've found a good setting for sharpening for tree leaves, grass, foliage that I think looks very natural, and is, in my admittedly limited data set, better even than Iridient Developer (which I still think is quite good).
So, here's an interesting comparison (and please don't ask for 100% crops, guys, 'cause I'm not going to put them up! Life's too short, fellas!
I'd be happy to post my sharpening settings that I find work well in the majority of cases). It's the same file shot with an X-Pro1 (sorry, my X-T1 is on it's way back to Fuji for the flare effect fix) and the Fuji 14mm converted from Fuji RAW with Iridient Developer 2.3.4, and Capture One 7.2.1
1) converted with Iridient Developer 2.3.4 to a TIFF, then imported for some subtle tweaks in LR 5.3
2) conversion with Capture One 7.2.1. Imported into Lightroom only to downsample to the output JPEG file size.
(Note: I was able to correct the keystoning of the 14mm lens in C1, but not in LR in the first photo; this is why the crops are slightly different.
As good as Iridient Developer is, in my opinion, Capture One 7.2.1 still does the best job of RAW conversion. While I'm not a pixel peeper, I did look at the foliage and grass closely at 100%, and am of the opinion that Capture One is a bit better than Iridient Developer than rendering what I consider to be a level of detail that has the requisite acutance yet is still natural-looking. But what I also notice that that Capture One holds detail in the clouds and in the shadow areas of the trees on the hills in the background notably better. And, IMHO, the photo, on the whole, looks more accurate and natural to what I remember the scene looking actually looking like (I just took this shot yesterday afternoon).
So, YMMV, but I still find Capture One to be my de-facto standard for X-trans (or any camera for that matter) RAW conversion. My second favorite is Iridient Developer, which I think also does a very good job.