Since the X-Pro1 and XE-1's X-Trans sensors haven't been analysed by DXOMark yet (perhaps because of issues from the differing sensor and RAW formats?), we'll have to wait and see. The X100s is likely the same sensor as the past two cameras, plus PDAF and an improved image processor and have been extraordinarily well received.
Low-pass filters on sensors lower pixel-level sharpness—hopefully we can agree with that. Unfortunately, they've been a reality since the Bayer pattern was invented in 1976 and put into use on camera sensors. A camera sensor either deals with color moiré or adds a low-pass filter, reducing sharpness. Until the Fuji X-Trans sensors, the only way to truly combat this was with big enough sesnsors (full frame). By solving the problem and removing the filter, a smaller sensor can resolve similar detail. We'll have to wait for the testing.
Regardless, this is an awesome backpacking camera. Easier to carry than an RX1, comes with an awesome optical and electronic hybrid viewfinder, has a built in ND filter (excellent for backpacking), and is a minimum of $1500 cheaper than the Sony RX1 (more when you consider getting an electronic viewfinder for it).
I think I'll likely be toting an X100s on the JMT this summer—excellent value proposition, size, and combination of features.