I've been shooting with the X-Trans sensor since the first day the X-Pro1 became available in April 2012. I've used it in the X-Pro and X-E1, which I've owned, and the X100s and XM1, which I had on loan for extended periods.
I've also spent the last several weeks with a loaner of a Nikon Df. The sensor in the Df is the best I've ever seen for everything except resolution. If resolution is your holy grail, you can't do better than the Sigma DP Merrill cameras but the D800 and A7r both come close. But it you want amazingly clean files at every ISO with great detail and color rendition up to ISO 12,800, the sensor in the Df and D4 is the best on the planet right now. I'm sure it will be bettered at some point, but if anyone really believes the X-Trans APS sensor lives up to that Df sensor, they're high on better drugs than I've ever taken (and I've taken my share in years past).
That said, for the Df to be a better overall choice for you, you either have to really value the tracking AF advantages that DSLRs still have over mirrorless (despite great strides in this area with the EM1 and reportedly the XT1) and/or you have to be willing to shoot pretty high end DSLR glass, which gets pretty large, heavy, and expensive. For single shot AF, the EM1 and GX7 and GH4 and other m43 bodies don't give up anything to DSLRs any longer. From reports, it sounds like the XT1 has either caught m43 in this regard or has at least closed the gap. For me, tracking AF is a non-issue, but for some its a big one and the DSLR is still a better choice.
In terms of lenses, I decided the only way I was gonna be OK with the larger and heavier Df was if I shot it with small primes. I did a lot of shooting with Nikon's "D" series lenses, which are as small or smaller than similar Fuji lenses and are also less expensive. Some of them are optically better than their Fuji counterparts (28mm vs the Fuji 18), some are not quite as good (Nikon 20 vs Fuji 14, Nikon 35 vs Fuji 23), but to me they're also good enough. BUT, they're slower than their Fuji counterparts, enough to about equalize on shallow DOF and to give back the roughly one stop advantage the Df sensor gets you. If I can shoot the Nikon 35mm at f2.0 at ISO 6400, I can shoot the Fuji 23mm at f1.4 at ISO 3200 and get roughly the same quality and DOF. Arguably the Df sensor is still a bit better, but at 6400 it's not notably better than the X-Trans at 3200 and at 12,800 it's not notably better than the X-Trans at 6400.
If you're willing to pay for and haul around the higher end DSLR glass, there's a clear benefit to the Df. After all, the Nikon 35mm f1.4 gains a full stop in terms of both shallow DOF and low light capability over the same Df with the 35mm f2.0 or the Fuji with the 23mm f1.4. But those are big, heavy, incredibly expensive lenses. I'm not willing to buy or carry those high end lenses, though, so the two cameras are close enough to a wash in terms of DOF and low light capability. Maybe a slight edge to the Nikon, but not enough to get worked up about.
The other thing is whether you prefer the shooting and handling characteristics of a DSLR or mirrorless. I prefer a big bright OVF to a big bright EVF, but I also love the advantages of a really good full time live view, particularly with a flip up rear screen. I like shooting both with and without a viewfinder, so if I have to take a slightly less wonderful electronic viewfinder to get the full live view experience, I'll take that. I can't seem to have the best of both worlds here (I was hopeful with the X-Pro, but too few Fuji lenses really work well with the OVF), so on balance mirrorless works better for me.
I love the battery life of the DSLR - really pretty eye-openingly great. BUT, that big flapping mirror and that big honking sensor also adds up to dust dust DUST!!! I'd never had to clean a camera's sensor before. I've been shooting m43 and Fuji and other mirrorless cameras for about four years now - never had to clean a sensor even once. I hadn't shot extensively with an SLR since the film days and obviously you don't have to clean THOSE sensors. With the Df, I was cloning out dust spots in the skies of almost all of my shots and cleaning the damn sensor every couple of days. I'd go out shooting with a clean sensor but by the time I was a couple of dozen shots into a shoot, dust spots started showing up. A lot of people have come to terms with this. Photography is my joy, not my job, and having to maintain the sensor like that makes it feel like more of a job.
Bottom line, if you're willing to pay the price for the best lenses and also willing to carry them around, the Df blows the doors off of any APS based camera, Fuji's included. But if you're not and you really want a smaller and lighter setup, you can do roughly as well with an APS mirrorless as you can with a full frame DSLR with the smaller, cheaper, lighter, slower lenses. I love much about the Df, but I'm gonna send it back after the loan period it and almost certainly buy an XT1.
-Ray
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