Given that the lens and sensor have been designed as a combination – which in many way is more crucial simply than the origin of the sensor - it's possible we might see the X100 convincingly outclassing the M9 (which of course will retain advantages in manual focusing and versatility).
I think that unlikely. Full frame sensors are in many ways less demanding on an optical system than smaller sensors (especially with respect to diffraction), especially when the lenses are designed for digital capture – as the most recent Leica, Nikon, Canon, and Zeiss FF lenses assuredly are.
I think it is realistic to hope for high-ISO output as good as the M9, perhaps better, and resolution as good, and likely better, than the M8.
A more fair comparison would pit the K-100 against 12-14 mpix APS-C cameras (D-300, D-90, Pentax K-x, etc), when those bodies are fitted with the best lenses for those systems: Nikon 24/1.4 (new), etc.
The little Fuji has some chance of approaching the performance of the best APS-C setups at a fraction of the price and a fraction of the bulk. As much as I might wish otherwise, it is unlikely to eclipse them.
But that level of performance is quite adequate for the things I'd use such a camera for. Used handheld, as the X-100 design obviously is intended to be used, camera movement will be the resolution-limiting parameter in this system –
not sensor or lens resolution.
For that reason, if I could wish to add one thing not found in the specs, it would be IS as effective as that found in the Olympus E-620, E-PL1, etc.