I pretty much agree with everything you said. I also have a D700 as my main camera, the IQ doesn't match it but it's pretty good considering it's like 1/4 or less the size and weight of a D700 with a 35mm attached (and much lighter than with 24-70 f/2.8). I took an 8 mile hike today with the X100 around my neck the whole way and it was fine, whereas even with my BlackRapid strap the D700 would have been tiring to carry. But it's the operational characteristics where the X100 is a big letdown, particularly the focusing (both auto and manual have lots of issues). Other issues for me:
-- EV dial is a bit loose, easily accidentally changed.
-- No manual ISO dial. I wish Fuji shipped an ISO dial that could replace the shutter dial or something because at least 90% of the time I'm in aperture priority mode and the shutter dial is useless. Auto ISO works decently, but I'd love easy manual control.
-- Could use one more assignable button. The RAW button would work, how many people actually use this? I'm guessing not many, generally either you are shooting RAW, or you aren't.
-- Battery is not only weak (I'm getting only about 150-250 shots per full charge on two different batteries, but it takes well over 3 hours to charge. That's horrible. My D700 battery isn't much bigger, gets 1600-2200 shots on a charge, and charges faster. Come on Fuji.
-- Startup times are very slow, for a fixed lens camera there is no excuse for a startup time that isn't nearly instant. It really seems like Fuji cheaped out on the processor used because the write times are also very slow, particularly for RAW. It feels like myTiVo, which while modern and HD, seems to use a 386 processor circa 1995.
-- The focus field indicators in the hybrid VF are not accurate for the given f-stop.
-- The nubs on the aperture ring get in my way when trying to use the very thin focusing ring.
-- The lens is REALLY prone to flaring, even with the lens hood, I basically have to use my hand to manually flag it if I'm shooting anywhere near the sun. And the lens hood doesn't work well. First, it's annoying you need an adapter and can't screw a filter right on the lens. So you put the adapter on, then a filter and the hood, what happens is the front surface of the filter ends up being even closer to the front of the hood, and since a filter is much larger than the lens glass itself, you end up being even worse off (flare-wise) when using the lens hood and a filter than with just the bare lens. They need to license Nikons nano coating for the lens, drop the filter adapter, and make a deeper hood.
Anyway, I'm keeping the X100 for now because it is vastly more convenient than the D700 in terms of will I have it with me or won't I? But it's got a long way to go too, it very much feels like the version 1.0 model that it is. I agree with the OP that, given all its issues it is a bit overpriced. For $700 or so I'd be a lot more willing to put up with its quirks. On the other hand, if they could fix all these issues, I might be willing to spend considerably more for it, maybe even up to $2K, especially if there's a full frame variant.