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What issues still remain? How is the Auto-ISO mode now?
Honestly, they're minor enough that I almost feel guilty mentioning them. I never bought an X100 because I found it frustrating when I tried to use it, but this camera is completely different in terms of responsiveness. Auto ISO is well done and I would love to see a similar implementation on the X-E1. It's not quite as slick as Nikon's implementation, but the ability to specify a minimum shutter speed is all I need to make it a useful feature. In good light, the AF seems pretty much as fast as the OM-D and the camera's startup and write speeds are greatly improved. Also, the smaller tweaks are very welcome, particularly the new location of the AF button, the addition of the Q menu, and the reordered positions of AF-C and AF-S on the focus switch. They've even tightened up some of the control dials so they're harder to accidentally bump.
As for issues that remain... Low light focus speed could still be better compared to the OM-D. I also still dislike like some of the controls, namely the spinning wheel on the back which seems the same as the X100's. I'd like to see a histogram in the instant image review. I can live with these things though.
Anyone who was interested in the X100 but was turned off by that camera's rough edges should take a look at the X100s. Fuji have done a good job refining the original concept.