Quiet leaf shutters have never been cheap, neither have parallax corrected OVFs, or EVFs, or wide f2 lenses, or new technology, or cameras aimed at small niche markets . Niche markets are used to pay a fair bit extra for their toys, so I think the x100 is actually cheap for what it is. Fuji was never the type of camera maker that tries to flood the mainstream market, Ca/So/Nikon will take care of that.
A more utilitarian way of looking at the price is taking the sum of its parts (going by B&H prices):
-Glass viewfinder (voigtlander $150)
-Electronic viewfinder (olympus $240)
-Autofocus 23/f2 lens for APS-C (closest I could think of was Nikon 24/2.8 for full frame $344)
-APS-C mirrorless body (NEX, I cant find one without lens, say $400?)
-Analog controls (?)
It all adds up quickly. I'm not subtracting anything for the fact that it is not interchangeable because this can be anything from a curse (for someone who wants to change lenses) to a blessing (for someone who generally doesnt). It is very hard to design a lens that is interchangeable & wide & f2 & pancake & keep the cost down & have manual controls & AF & digital with good quality for the specific size sensor. If you look at the lens line up for NEX or M4:3 you will find that they dont actually have a lens with all of the above specs. Besides, 35/2 is the most popular lens in the small/RF camera world, and most people buying will be either street shooters or DSLR/RF owners with a range of lenses to cover all their other needs. Niche product for a niche market.