I have the Fuji X100s (same sensor as the XT-1) in addition to my Pentax K5 and a bunch of lenses. I'm not selling/switching Pentax over to Fuji as I don't see a dramatic difference in 16mp quality between the two. I have not switched to K3 yet as I don't need the megapixels and I don't really have an issue focusing with the K5 (I manual focus a lot anyway). Fuji does surpass the K5's sensor in sharpness and high iso performance. The difference is less in RAW but pretty dramatic in JPEG's. Fuji has excellent (probably the best) JPEG's with the film simulation. The 23mm on the X100s is better than my DA 16-50 taking images at the same length. (It's a prime). Another "feature" of the Fuji Jpegs's is file size, they are often only 3-5mb which is tiny for jpeg's out of modern cameras. I don't bother with RAW on the Fuji, it's jpegs are that good. I would rather have an EVF at this point than prism, if you haven't seen a good one check out the XT-1 (X100s is slightly laggy but has a optical as well which is really big and bright like a full frame) EVF has come a long way and has big advantages over prisms like seeing your changes in real time and much easier manual focus, worlds easier. I think the hybrid viewfinder is pretty much awesome and I do think mirrorless is the future with how good these EVF's are getting. I'm not ditching the Pentax for Fuji unless the XT-1 evolves into something amazing on the next round. In the end I get great shot's from either, I do enjoy the X100s for a "grab and go" light camera with a really cool viewfinder and old fashioned dials.
Fuji is a bit sharper and bit better in the ISO dept. At ISO lower than 800 the Fuji is just sharper and I prefer it's colors strait from the camera. Results would be similar from the XT-1 at 23mm. This is the best 16mp out there imo at this time and probably the best high iso APS-C. In the end lightroom render's the difference negligible (including FF other than DOF) for the most part so pick the camera that handles good and inspires you to use it!
Here is a ISO 6400 RAW shot from both. (negligible imo up to this iso)
Fuji on the left, Pentax right (DA*16-50 at 23mm)
ISO 6400 1/160th 2.8 on both
JPEG ISO 12800 and 25600 (Fuji max) strait from the camera, pretty dramatic JPEG difference. (I honestly never shoot this high an ISO with either, 6400 is about as high as I ever need).